star/star_align_reads

align

fasta

genome

Description

Aligns reads to a reference genome using STAR.

Type

python_script

License

MIT

Keywords

align

fasta

genome

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
aligned_reads: "$id.$key.aligned_reads.bam"  
reads_per_gene: "$id.$key.reads_per_gene.tsv"  
unmapped: "$id.$key.unmapped.fastq"  
unmapped_r2: "$id.$key.unmapped_r2.fastq"  
chimeric_junctions: "$id.$key.chimeric_junctions.tsv"  
log: "$id.$key.log.txt"  
splice_junctions: "$id.$key.splice_junctions.tsv"  
reads_aligned_to_transcriptome: "$id.$key.reads_aligned_to_transcriptome.bam"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.1 \  
  -main-script target/nextflow/star/star_align_reads/main.nf \  
  -params-file params.yaml

Run Parameters

Name	Type & Properties	Description
--run_rng_seed	integer	random number generator seed.

Name

Type & Properties

--run_rng_seed

integer

Genome Parameters

Name	Type & Properties	Description
--genome_dir	file required	path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome)
--genome_load	string	mode of shared memory usage for the genome files. Only used with --runMode alignReads. - LoadAndKeep ... load genome into shared and keep it in memory after run - LoadAndRemove ... load genome into shared but remove it after run - LoadAndExit ... load genome into shared memory and exit, keeping the genome in memory for future runs - Remove ... do not map anything, just remove loaded genome from memory - NoSharedMemory ... do not use shared memory, each job will have its own private copy of the genome
--genome_fasta_files	file multiple	path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they cannot be zipped. Required for the genome generation (--runMode genomeGenerate). Can also be used in the mapping (--runMode alignReads) to add extra (new) sequences to the genome (e.g. spike-ins).
--genome_file_sizes	integer multiple	genome files exact sizes in bytes. Typically, this should not be defined by the user.
--genome_transform_output	string multiple	which output to transform back to original genome - SAM ... SAM/BAM alignments - SJ ... splice junctions (SJ.out.tab) - Quant ... quantifications (from --quant_mode option) - None ... no transformation of the output
--genome_chr_set_mitochondrial	string multiple	names of the mitochondrial chromosomes. Presently only used for STARsolo statistics output/

Name

Type & Properties

--genome_dir

file

required

--genome_load

string

--genome_fasta_files

file

multiple

--genome_file_sizes

integer

multiple

--genome_transform_output

string

multiple

--genome_chr_set_mitochondrial

string

multiple

Splice Junctions Database

Name	Type & Properties	Description
--sjdb_file_chr_start_end	string multiple	path to the files with genomic coordinates (chr <tab> start <tab> end <tab> strand) for the splice junction introns. Multiple files can be supplied and will be concatenated.
--sjdb_gtf_file	file	path to the GTF file with annotations
--sjdb_gtf_chr_prefix	string	prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC genomes)
--sjdb_gtf_feature_exon	string	feature type in GTF file to be used as exons for building transcripts
--sjdb_gtf_tag_exon_parent_transcript	string	GTF attribute name for parent transcript ID (default "transcript_id" works for GTF files)
--sjdb_gtf_tag_exon_parent_gene	string	GTF attribute name for parent gene ID (default "gene_id" works for GTF files)
--sjdb_gtf_tag_exon_parent_gene_name	string multiple	GTF attribute name for parent gene name
--sjdb_gtf_tag_exon_parent_gene_type	string multiple	GTF attribute name for parent gene type
--sjdb_overhang	integer	length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)
--sjdb_score	integer	extra alignment score for alignments that cross database junctions
--sjdb_insert_save	string	which files to save when sjdb junctions are inserted on the fly at the mapping step - Basic ... only small junction / transcript files - All ... all files including big Genome, SA and SAindex - this will create a complete genome directory

Name

Type & Properties

--sjdb_file_chr_start_end

string

multiple

--sjdb_gtf_file

file

--sjdb_gtf_chr_prefix

string

--sjdb_gtf_feature_exon

string

--sjdb_gtf_tag_exon_parent_transcript

string

--sjdb_gtf_tag_exon_parent_gene

string

--sjdb_gtf_tag_exon_parent_gene_name

string

multiple

--sjdb_gtf_tag_exon_parent_gene_type

string

multiple

--sjdb_overhang

integer

--sjdb_score

integer

--sjdb_insert_save

string

Variation parameters

Name	Type & Properties	Description
--var_vcf_file	string	path to the VCF file that contains variation data. The 10th column should contain the genotype information, e.g. 0/1

Name

Type & Properties

--var_vcf_file

string

Read Parameters

Name	Type & Properties	Description
--read_files_type	string	format of input read files - Fastx ... FASTA or FASTQ - SAM SE ... SAM or BAM single-end reads; for BAM use --read_files_command samtools view - SAM PE ... SAM or BAM paired-end reads; for BAM use --read_files_command samtools view
--read_files_sam_attr_keep	string multiple	for --read_files_type SAM SE/PE, which SAM tags to keep in the output BAM, e.g.: --readFilesSAMtagsKeep RG PL - All ... keep all tags - None ... do not keep any tags
--read_files_manifest	file	path to the "manifest" file with the names of read files. The manifest file should contain 3 tab-separated columns: paired-end reads: read1_file_name $tab$ read2_file_name $tab$ read_group_line. single-end reads: read1_file_name $tab$ - $tab$ read_group_line. Spaces, but not tabs are allowed in file names. If read_group_line does not start with ID:, it can only contain one ID field, and ID: will be added to it. If read_group_line starts with ID:, it can contain several fields separated by $tab$, and all fields will be be copied verbatim into SAM @RG header line.
--read_files_prefix	string	prefix for the read files names, i.e. it will be added in front of the strings in --readFilesIn
--read_files_command	string multiple	command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.
--read_map_number	integer	number of reads to map from the beginning of the file -1: map all reads
--read_mates_lengths_in	string	Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations.
--read_name_separator	string multiple	character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)
--read_quality_score_base	integer	number to be subtracted from the ASCII code to get Phred quality score

Name

Type & Properties

--read_files_type

string

--read_files_sam_attr_keep

string

multiple

--read_files_manifest

file

--read_files_prefix

string

--read_files_command

string

multiple

--read_map_number

integer

--read_mates_lengths_in

string

--read_name_separator

string

multiple

--read_quality_score_base

integer

Read Clipping

Name	Type & Properties	Description
--clip_adapter_type	string	adapter clipping type - Hamming ... adapter clipping based on Hamming distance, with the number of mismatches controlled by --clip5pAdapterMMp - CellRanger4 ... 5p and 3p adapter clipping similar to CellRanger4. Utilizes Opal package by Martin Sosic: https://github.com/Martinsos/opal - None ... no adapter clipping, all other clip* parameters are disregarded
--clip3p_nbases	integer multiple	number(s) of bases to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates.
--clip3p_adapter_seq	string multiple	adapter sequences to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates. - polyA ... polyA sequence with the length equal to read length
--clip3p_adapter_mm_p	double multiple	max proportion of mismatches for 3p adapter clipping for each mate. If one value is given, it will be assumed the same for both mates.
--clip3p_after_adapter_nbases	integer multiple	number of bases to clip from 3p of each mate after the adapter clipping. If one value is given, it will be assumed the same for both mates.
--clip5p_nbases	integer multiple	number(s) of bases to clip from 5p of each mate. If one value is given, it will be assumed the same for both mates.

Name

Type & Properties

--clip_adapter_type

string

--clip3p_nbases

integer

multiple

--clip3p_adapter_seq

string

multiple

--clip3p_adapter_mm_p

double

multiple

--clip3p_after_adapter_nbases

integer

multiple

--clip5p_nbases

integer

multiple

Limits

Name	Type & Properties	Description
--limit_genome_generate_ram	long	maximum available RAM (bytes) for genome generation
--limit_io_buffer_size	long multiple	max available buffers size (bytes) for input/output, per thread
--limit_out_sam_one_read_bytes	long	max size of the SAM record (bytes) for one read. Recommended value: >(2(LengthMate1+LengthMate2+100)outFilterMultimapNmax
--limit_out_sj_one_read	integer	max number of junctions for one read (including all multi-mappers)
--limit_out_sj_collapsed	integer	max number of collapsed junctions
--limit_bam_sort_ram	long	maximum available RAM (bytes) for sorting BAM. If =0, it will be set to the genome index size. 0 value can only be used with --genome_load NoSharedMemory option.
--limit_sjdb_insert_nsj	integer	maximum number of junctions to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run
--limit_nreads_soft	integer	soft limit on the number of reads

Name

Type & Properties

--limit_genome_generate_ram

long

--limit_io_buffer_size

long

multiple

--limit_out_sam_one_read_bytes

long

--limit_out_sj_one_read

integer

--limit_out_sj_collapsed

integer

--limit_bam_sort_ram

long

--limit_sjdb_insert_nsj

integer

--limit_nreads_soft

integer

Output: general

Name	Type & Properties	Description
--out_tmp_keep	string	whether to keep the temporary files after STAR runs is finished - None ... remove all temporary files - All ... keep all files
--out_std	string	which output will be directed to stdout (standard out) - Log ... log messages - SAM ... alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out - BAM_Unsorted ... alignments in BAM format, unsorted. Requires --out_sam_type BAM Unsorted - BAM_SortedByCoordinate ... alignments in BAM format, sorted by coordinate. Requires --out_sam_type BAM SortedByCoordinate - BAM_Quant ... alignments to transcriptome in BAM format, unsorted. Requires --quant_mode TranscriptomeSAM
--out_reads_unmapped	string	output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s). - None ... no output - Fastx ... output in separate fasta/fastq files, Unmapped.out.mate1/2
--out_qs_conversion_add	integer	add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)
--out_multimapper_order	string	order of multimapping alignments in the output files - Old_2.4 ... quasi-random order used before 2.5.0 - Random ... random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases.

Name

Type & Properties

--out_tmp_keep

string

--out_std

string

--out_reads_unmapped

string

--out_qs_conversion_add

integer

--out_multimapper_order

string

Output: SAM and BAM

Name	Type & Properties	Description
--out_sam_type	string multiple	type of SAM/BAM output 1st word: - BAM ... output BAM without sorting - SAM ... output SAM without sorting - None ... no SAM/BAM output 2nd, 3rd: - Unsorted ... standard unsorted - SortedByCoordinate ... sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limit_bam_sort_ram.
--out_sam_mode	string	mode of SAM output - None ... no SAM output - Full ... full SAM output - NoQS ... full SAM but without quality scores
--out_sam_strand_field	string	Cufflinks-like strand field flag - None ... not used - intronMotif ... strand derived from the intron motif. This option changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out.
--out_sam_attributes	string multiple	a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order. *Presets: - None ... no attributes - Standard ... NH HI AS nM - All ... NH HI AS nM NM MD jM jI MC ch Alignment: - NH ... number of loci the reads maps to: =1 for unique mappers, >1 for multimappers. Standard SAM tag. - HI ... multiple alignment index, starts with --out_sam_attr_ih_start (=1 by default). Standard SAM tag. - AS ... local alignment score, +1/-1 for matches/mismateches, score penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag. - nM ... number of mismatches. For PE reads, sum over two mates. - NM ... edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag. - MD ... string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag. - jM ... intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value. - jI ... start and end of introns for all junctions (1-based). - XS ... alignment strand according to --out_sam_strand_field. - MC ... mate's CIGAR string. Standard SAM tag. - ch ... marks all segment of all chimeric alingments for --chim_out_type WithinBAM output. - cN ... number of bases clipped from the read ends: 5' and 3' *Variation: - vA ... variant allele - vG ... genomic coordinate of the variant overlapped by the read. - vW ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --wasp_output_mode SAMtag. - ha ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid . STARsolo: - CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo demultiplexing. - GX GN ... gene ID and gene name for unique-gene reads. - gx gn ... gene IDs and gene names for unique- and multi-gene reads. - CB UB ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --out_sam_type BAM SortedByCoordinate. - sM ... assessment of CB and UMI. - sS ... sequence of the entire barcode (CB,UMI,adapter). - sQ ... quality of the entire barcode. - sF ... type of feature overlap and number of features for each alignment ***Unsupported/undocumented: - rB ... alignment block read/genomic coordinates. - vR ... read coordinate of the variant.
--out_sam_attr_ih_start	integer	start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie.
--out_sam_unmapped	string multiple	output of unmapped reads in the SAM format 1st word: - None ... no output - Within ... output unmapped reads within the main SAM file (i.e. Aligned.out.sam) 2nd word: - KeepPairs ... record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only affects multi-mapping reads.
--out_sam_order	string	type of sorting for the SAM output Paired: one mate after the other for all paired alignments PairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files
--out_sam_primary_flag	string	which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG - OneBestScore ... only one alignment with the best score is primary - AllBestScore ... all alignments with the best score are primary
--out_sam_read_id	string	read ID record type - Standard ... first word (until space) from the FASTx read ID line, removing /1,/2 from the end - Number ... read number (index) in the FASTx file
--out_sam_mapq_unique	integer	0 to 255: the MAPQ value for unique mappers
--out_sam_flag_or	integer	0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e. FLAG=FLAG \| outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise.
--out_sam_flag_and	integer	0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e. FLAG=FLAG & outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise.
--out_sam_attr_rg_line	string multiple	SAM/BAM read group line. The first word contains the read group identifier and must start with "ID:", e.g. --out_sam_attr_rg_line ID:xxx CN:yy "DS:z z z". xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted. Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g. --out_sam_attr_rg_line ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy
--out_sam_header_hd	string multiple	@HD (header) line of the SAM header
--out_sam_header_pg	string multiple	extra @PG (software) line of the SAM header (in addition to STAR)
--out_sam_header_comment_file	string	path to the file with @CO (comment) lines of the SAM header
--out_sam_filter	string multiple	filter the output into main SAM/BAM files - KeepOnlyAddedReferences ... only keep the reads for which all alignments are to the extra reference sequences added with --genome_fasta_files at the mapping stage. - KeepAllAddedReferences ... keep all alignments to the extra reference sequences added with --genome_fasta_files at the mapping stage.
--out_sam_mult_nmax	integer	max number of multiple alignments for a read that will be output to the SAM/BAM files. Note that if this value is not equal to -1, the top scoring alignment will be output first - -1 ... all alignments (up to --out_filter_multimap_nmax) will be output
--out_sam_tlen	integer	calculation method for the TLEN field in the SAM/BAM files - 1 ... leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate - 2 ... leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends
--out_bam_compression	integer	-1 to 10 BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression
--out_bam_sorting_thread_n	integer	>=0: number of threads for BAM sorting. 0 will default to min(6,--runThreadN).
--out_bam_sorting_bins_n	integer	>0: number of genome bins for coordinate-sorting

Name

Type & Properties

--out_sam_type

string

multiple

--out_sam_mode

string

--out_sam_strand_field

string

--out_sam_attributes

string

multiple

a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order. ***Presets: - None ... no attributes - Standard ... NH HI AS nM - All ... NH HI AS nM NM MD jM jI MC ch ***Alignment: - NH ... number of loci the reads maps to: =1 for unique mappers, >1 for multimappers. Standard SAM tag. - HI ... multiple alignment index, starts with --out_sam_attr_ih_start (=1 by default). Standard SAM tag. - AS ... local alignment score, +1/-1 for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag. - nM ... number of mismatches. For PE reads, sum over two mates. - NM ... edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag. - MD ... string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag. - jM ... intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value. - jI ... start and end of introns for all junctions (1-based). - XS ... alignment strand according to --out_sam_strand_field. - MC ... mate's CIGAR string. Standard SAM tag. - ch ... marks all segment of all chimeric alingments for --chim_out_type WithinBAM output. - cN ... number of bases clipped from the read ends: 5' and 3' ***Variation: - vA ... variant allele - vG ... genomic coordinate of the variant overlapped by the read. - vW ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --wasp_output_mode SAMtag. - ha ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid . ***STARsolo: - CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing. - GX GN ... gene ID and gene name for unique-gene reads. - gx gn ... gene IDs and gene names for unique- and multi-gene reads. - CB UB ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --out_sam_type BAM SortedByCoordinate. - sM ... assessment of CB and UMI. - sS ... sequence of the entire barcode (CB,UMI,adapter). - sQ ... quality of the entire barcode. - sF ... type of feature overlap and number of features for each alignment ***Unsupported/undocumented: - rB ... alignment block read/genomic coordinates. - vR ... read coordinate of the variant.

--out_sam_attr_ih_start

integer

--out_sam_unmapped

string

multiple

--out_sam_order

string

--out_sam_primary_flag

string

--out_sam_read_id

string

--out_sam_mapq_unique

integer

--out_sam_flag_or

integer

--out_sam_flag_and

integer

--out_sam_attr_rg_line

string

multiple

--out_sam_header_hd

string

multiple

--out_sam_header_pg

string

multiple

--out_sam_header_comment_file

string

--out_sam_filter

string

multiple

--out_sam_mult_nmax

integer

--out_sam_tlen

integer

--out_bam_compression

integer

--out_bam_sorting_thread_n

integer

--out_bam_sorting_bins_n

integer

BAM processing

Name	Type & Properties	Description
--bam_remove_duplicates_type	string	mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only - - ... no duplicate removal/marking - UniqueIdentical ... mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical - UniqueIdenticalNotMulti ... mark duplicate unique mappers but not multimappers.
--bam_remove_duplicates_mate2bases_n	integer	number of bases from the 5' of mate 2 to use in collapsing (e.g. for RAMPAGE)

Name

Type & Properties

--bam_remove_duplicates_type

string

--bam_remove_duplicates_mate2bases_n

integer

Output Wiggle

Name	Type & Properties	Description
--out_wig_type	string multiple	type of signal output, e.g. "bedGraph" OR "bedGraph read1_5p". Requires sorted BAM: --out_sam_type BAM SortedByCoordinate . 1st word: - None ... no signal output - bedGraph ... bedGraph format - wiggle ... wiggle format 2nd word: - read1_5p ... signal from only 5' of the 1st read, useful for CAGE/RAMPAGE etc - read2 ... signal from only 2nd read
--out_wig_strand	string	strandedness of wiggle/bedGraph output - Stranded ... separate strands, str1 and str2 - Unstranded ... collapsed strands
--out_wig_references_prefix	string	prefix matching reference names to include in the output wiggle file, e.g. "chr", default "-" - include all references
--out_wig_norm	string	type of normalization for the signal - RPM ... reads per million of mapped reads - None ... no normalization, "raw" counts

Name

Type & Properties

--out_wig_type

string

multiple

--out_wig_strand

string

--out_wig_references_prefix

string

--out_wig_norm

string

Output Filtering

Name	Type & Properties	Description
--out_filter_type	string	type of filtering - Normal ... standard filtering using only current alignment - BySJout ... keep only those reads that contain junctions that passed filtering into SJ.out.tab
--out_filter_multimap_score_range	integer	the score range below the maximum score for multimapping alignments
--out_filter_multimap_nmax	integer	maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value. Otherwise no alignments will be output, and the read will be counted as "mapped to too many loci" in the Log.final.out .
--out_filter_mismatch_nmax	integer	alignment will be output only if it has no more mismatches than this value.
--out_filter_mismatch_nover_lmax	double	alignment will be output only if its ratio of mismatches to mapped length is less than or equal to this value.
--out_filter_mismatch_nover_read_lmax	double	alignment will be output only if its ratio of mismatches to read length is less than or equal to this value.
--out_filter_score_min	integer	alignment will be output only if its score is higher than or equal to this value.
--out_filter_score_min_over_lread	double	same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for paired-end reads)
--out_filter_match_nmin	integer	alignment will be output only if the number of matched bases is higher than or equal to this value.
--out_filter_match_nmin_over_lread	double	sam as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads).
--out_filter_intron_motifs	string	filter alignment using their motifs - None ... no filtering - RemoveNoncanonical ... filter out alignments that contain non-canonical junctions - RemoveNoncanonicalUnannotated ... filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept.
--out_filter_intron_strands	string	filter alignments - RemoveInconsistentStrands ... remove alignments that have junctions with inconsistent strands - None ... no filtering

Name

Type & Properties

--out_filter_type

string

--out_filter_multimap_score_range

integer

--out_filter_multimap_nmax

integer

--out_filter_mismatch_nmax

integer

--out_filter_mismatch_nover_lmax

double

--out_filter_mismatch_nover_read_lmax

double

--out_filter_score_min

integer

--out_filter_score_min_over_lread

double

--out_filter_match_nmin

integer

--out_filter_match_nmin_over_lread

double

--out_filter_intron_motifs

string

--out_filter_intron_strands

string

Output splice junctions (SJ.out.tab)

Name	Type & Properties	Description
--out_sj_type	string	type of splice junction output - Standard ... standard SJ.out.tab output - None ... no splice junction output

Name

Type & Properties

--out_sj_type

string

Output Filtering: Splice Junctions

Name	Type & Properties	Description
--out_sj_filter_reads	string	which reads to consider for collapsed splice junctions output - All ... all reads, unique- and multi-mappers - Unique ... uniquely mapping reads only
--out_sj_filter_overhang_min	integer multiple	minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif does not apply to annotated junctions
--out_sj_filter_count_unique_min	integer multiple	minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied does not apply to annotated junctions
--out_sj_filter_count_total_min	integer multiple	minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied does not apply to annotated junctions
--out_sj_filter_dist_to_other_sj_min	integer multiple	minimum allowed distance to other junctions' donor/acceptor does not apply to annotated junctions
--out_sj_filter_intron_max_vs_read_n	integer multiple	maximum gap allowed for junctions supported by 1,2,3,,,N reads i.e. by default junctions supported by 1 read can have gaps <=50000b, by 2 reads: <=100000b, by 3 reads: <=200000. by >=4 reads any gap <=alignIntronMax does not apply to annotated junctions

Name

Type & Properties

--out_sj_filter_reads

string

--out_sj_filter_overhang_min

integer

multiple

--out_sj_filter_count_unique_min

integer

multiple

--out_sj_filter_count_total_min

integer

multiple

--out_sj_filter_dist_to_other_sj_min

integer

multiple

--out_sj_filter_intron_max_vs_read_n

integer

multiple

Scoring

Name	Type & Properties	Description
--score_gap	integer	splice junction penalty (independent on intron motif)
--score_gap_noncan	integer	non-canonical junction penalty (in addition to scoreGap)
--score_gap_gcag	integer	GC/AG and CT/GC junction penalty (in addition to scoreGap)
--score_gap_atac	integer	AT/AC and GT/AT junction penalty (in addition to scoreGap)
--score_genomic_length_log2scale	integer	extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)
--score_del_open	integer	deletion open penalty
--score_del_base	integer	deletion extension penalty per base (in addition to scoreDelOpen)
--score_ins_open	integer	insertion open penalty
--score_ins_base	integer	insertion extension penalty per base (in addition to scoreInsOpen)
--score_stitch_sj_shift	integer	maximum score reduction while searching for SJ boundaries in the stitching step

Name

Type & Properties

--score_gap

integer

--score_gap_noncan

integer

--score_gap_gcag

integer

--score_gap_atac

integer

--score_genomic_length_log2scale

integer

--score_del_open

integer

--score_del_base

integer

--score_ins_open

integer

--score_ins_base

integer

--score_stitch_sj_shift

integer

Alignments and Seeding

Name	Type & Properties	Description
--seed_search_start_lmax	integer	defines the search start point through the read - the read is split into pieces no longer than this value
--seed_search_start_lmax_over_lread	double	seedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads)
--seed_search_lmax	integer	defines the maximum length of the seeds, if =0 seed length is not limited
--seed_multimap_nmax	integer	only pieces that map fewer than this value are utilized in the stitching procedure
--seed_per_read_nmax	integer	max number of seeds per read
--seed_per_window_nmax	integer	max number of seeds per window
--seed_none_loci_per_window	integer	max number of one seed loci per window
--seed_split_min	integer	min length of the seed sequences split by Ns or mate gap
--seed_map_min	integer	min length of seeds to be mapped
--align_intron_min	integer	minimum intron size, genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion
--align_intron_max	integer	maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins
--align_mates_gap_max	integer	maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins
--align_sj_overhang_min	integer	minimum overhang (i.e. block size) for spliced alignments
--align_sj_stitch_mismatch_nmax	integer multiple	maximum number of mismatches for stitching of the splice junctions (-1: no limit). (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif.
--align_sjdb_overhang_min	integer	minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments
--align_spliced_mate_map_lmin	integer	minimum mapped length for a read mate that is spliced
--align_spliced_mate_map_lmin_over_lmate	double	alignSplicedMateMapLmin normalized to mate length
--align_windows_per_read_nmax	integer	max number of windows per read
--align_transcripts_per_window_nmax	integer	max number of transcripts per window
--align_transcripts_per_read_nmax	integer	max number of different alignments per read to consider
--align_ends_type	string	type of read ends alignment - Local ... standard local alignment with soft-clipping allowed - EndToEnd ... force end-to-end read alignment, do not soft-clip - Extend5pOfRead1 ... fully extend only the 5p of the read1, all other ends: local alignment - Extend5pOfReads12 ... fully extend only the 5p of the both read1 and read2, all other ends: local alignment
--align_ends_protrude	string	allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate 1st word: int: maximum number of protrusion bases allowed 2nd word: string: - ConcordantPair ... report alignments with non-zero protrusion as concordant pairs - DiscordantPair ... report alignments with non-zero protrusion as discordant pairs
--align_soft_clip_at_reference_ends	string	allow the soft-clipping of the alignments past the end of the chromosomes - Yes ... allow - No ... prohibit, useful for compatibility with Cufflinks
--align_insertion_flush	string	how to flush ambiguous insertion positions - None ... insertions are not flushed - Right ... insertions are flushed to the right

Name

Type & Properties

--seed_search_start_lmax

integer

--seed_search_start_lmax_over_lread

double

--seed_search_lmax

integer

--seed_multimap_nmax

integer

--seed_per_read_nmax

integer

--seed_per_window_nmax

integer

--seed_none_loci_per_window

integer

--seed_split_min

integer

--seed_map_min

integer

--align_intron_min

integer

--align_intron_max

integer

--align_mates_gap_max

integer

--align_sj_overhang_min

integer

--align_sj_stitch_mismatch_nmax

integer

multiple

--align_sjdb_overhang_min

integer

--align_spliced_mate_map_lmin

integer

--align_spliced_mate_map_lmin_over_lmate

double

--align_windows_per_read_nmax

integer

--align_transcripts_per_window_nmax

integer

--align_transcripts_per_read_nmax

integer

--align_ends_type

string

--align_ends_protrude

string

--align_soft_clip_at_reference_ends

string

--align_insertion_flush

string

Paired-End reads

Name	Type & Properties	Description
--pe_overlap_nbases_min	integer	minimum number of overlapping bases to trigger mates merging and realignment. Specify >0 value to switch on the "merginf of overlapping mates" algorithm.
--pe_overlap_mm_p	double	maximum proportion of mismatched bases in the overlap area

Name

Type & Properties

--pe_overlap_nbases_min

integer

--pe_overlap_mm_p

double

Windows, Anchors, Binning

Name	Type & Properties	Description
--win_anchor_multimap_nmax	integer	max number of loci anchors are allowed to map to
--win_bin_nbits	integer	=log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins.
--win_anchor_dist_nbins	integer	max number of bins between two anchors that allows aggregation of anchors into one window
--win_flank_nbins	integer	log2(winFlank), where win Flank is the size of the left and right flanking regions for each window
--win_read_coverage_relative_min	double	minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only.
--win_read_coverage_bases_min	integer	minimum number of bases covered by the seeds in a window , for STARlong algorithm only.

Name

Type & Properties

--win_anchor_multimap_nmax

integer

--win_bin_nbits

integer

--win_anchor_dist_nbins

integer

--win_flank_nbins

integer

--win_read_coverage_relative_min

double

--win_read_coverage_bases_min

integer

Chimeric Alignments

Name	Type & Properties	Description
--chim_out_type	string multiple	type of chimeric output - Junctions ... Chimeric.out.junction - SeparateSAMold ... output old SAM into separate Chimeric.out.sam file - WithinBAM ... output into main aligned BAM files (Aligned.*.bam) - WithinBAM HardClip ... (default) hard-clipping in the CIGAR for supplemental chimeric alignments (default if no 2nd word is present) - WithinBAM SoftClip ... soft-clipping in the CIGAR for supplemental chimeric alignments
--chim_segment_min	integer	minimum length of chimeric segment length, if ==0, no chimeric output
--chim_score_min	integer	minimum total (summed) score of the chimeric segments
--chim_score_drop_max	integer	max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length
--chim_score_separation	integer	minimum difference (separation) between the best chimeric score and the next one
--chim_score_junction_non_gtag	integer	penalty for a non-GT/AG chimeric junction
--chim_junction_overhang_min	integer	minimum overhang for a chimeric junction
--chim_segment_read_gap_max	integer	maximum gap in the read sequence between chimeric segments
--chim_filter	string multiple	different filters for chimeric alignments - None ... no filtering - banGenomicN ... Ns are not allowed in the genome sequence around the chimeric junction
--chim_main_segment_mult_nmax	integer	maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments.
--chim_multimap_nmax	integer	maximum number of chimeric multi-alignments - 0 ... use the old scheme for chimeric detection which only considered unique alignments
--chim_multimap_score_range	integer	the score range for multi-mapping chimeras below the best chimeric score. Only works with --chim_multimap_nmax > 1
--chim_nonchim_score_drop_min	integer	to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value
--chim_out_junction_format	integer	formatting type for the Chimeric.out.junction file - 0 ... no comment lines/headers - 1 ... comment lines at the end of the file: command line and Nreads: total, unique/multi-mapping

Name

Type & Properties

--chim_out_type

string

multiple

--chim_segment_min

integer

--chim_score_min

integer

--chim_score_drop_max

integer

--chim_score_separation

integer

--chim_score_junction_non_gtag

integer

--chim_junction_overhang_min

integer

--chim_segment_read_gap_max

integer

--chim_filter

string

multiple

--chim_main_segment_mult_nmax

integer

--chim_multimap_nmax

integer

--chim_multimap_score_range

integer

--chim_nonchim_score_drop_min

integer

--chim_out_junction_format

integer

Quantification of Annotations

Name	Type & Properties	Description
--quant_mode	string multiple	types of quantification requested - - ... none - TranscriptomeSAM ... output SAM/BAM alignments to transcriptome into a separate file - GeneCounts ... count reads per gene
--quant_transcriptome_bam_compression	integer	-2 to 10 transcriptome BAM compression level - -2 ... no BAM output - -1 ... default compression (6?) - 0 ... no compression - 10 ... maximum compression
--quant_transcriptome_sam_output	string	alignment filtering for TranscriptomeSAM output - BanSingleEnd_BanIndels_ExtendSoftclip ... prohibit indels and single-end alignments, extend softclips - compatible with RSEM - BanSingleEnd ... prohibit single-end alignments, allow indels and softclips - BanSingleEnd_ExtendSoftclip ... prohibit single-end alignments, extend softclips, allow indels

Name

Type & Properties

--quant_mode

string

multiple

--quant_transcriptome_bam_compression

integer

--quant_transcriptome_sam_output

string

2-pass Mapping

Name	Type & Properties	Description
--twopass_mode	string	2-pass mapping mode. - None ... 1-pass mapping - Basic ... basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly
--twopass1reads_n	integer	number of reads to process for the 1st step. Use very large number (or default -1) to map all reads in the first step.

Name

Type & Properties

--twopass_mode

string

--twopass1reads_n

integer

WASP parameters

Name	Type & Properties	Description
--wasp_output_mode	string	WASP allele-specific output type. This is re-implementation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061-1063 (2015), https://www.nature.com/articles/nmeth.3582 . - SAMtag ... add WASP tags to the alignments that pass WASP filtering

Name

Type & Properties

--wasp_output_mode

string

STARsolo (single cell RNA-seq) parameters

Name	Type & Properties	Description
--solo_type	string multiple	type of single-cell RNA-seq - CB_UMI_Simple ... (a.k.a. Droplet) one UMI and one Cell Barcode of fixed length in read2, e.g. Drop-seq and 10X Chromium. - CB_UMI_Complex ... multiple Cell Barcodes of varying length, one UMI of fixed length and one adapter sequence of fixed length are allowed in read2 only (e.g. inDrop, ddSeq). - CB_samTagOut ... output Cell Barcode as CR and/or CB SAm tag. No UMI counting. --readFilesIn cDNA_read1 [cDNA_read2 if paired-end] CellBarcode_read . Requires --out_sam_type BAM Unsorted [and/or SortedByCoordinate] - SmartSeq ... Smart-seq: each cell in a separate FASTQ (paired- or single-end), barcodes are corresponding read-groups, no UMI sequences, alignments deduplicated according to alignment start and end (after extending soft-clipped bases)
--solo_cb_type	string	cell barcode type Sequence: cell barcode is a sequence (standard option) String: cell barcode is an arbitrary string
--solo_cb_whitelist	string multiple	file(s) with whitelist(s) of cell barcodes. Only --solo_type CB_UMI_Complex allows more than one whitelist file. - None ... no whitelist: all cell barcodes are allowed
--solo_cb_start	integer	cell barcode start base
--solo_cb_len	integer	cell barcode length
--solo_umi_start	integer	UMI start base
--solo_umi_len	integer	UMI length
--solo_barcode_read_length	integer	length of the barcode read - 1 ... equal to sum of soloCBlen+soloUMIlen - 0 ... not defined, do not check
--solo_barcode_mate	integer	identifies which read mate contains the barcode (CB+UMI) sequence - 0 ... barcode sequence is on separate read, which should always be the last file in the --readFilesIn listed - 1 ... barcode sequence is a part of mate 1 - 2 ... barcode sequence is a part of mate 2
--solo_cb_position	string multiple	position of Cell Barcode(s) on the barcode read. Presently only works with --solo_type CB_UMI_Complex, and barcodes are assumed to be on Read2. Format for each barcode: startAnchor_startPosition_endAnchor_endPosition start(end)Anchor defines the Anchor Base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end start(end)Position is the 0-based position with of the CB start(end) with respect to the Anchor Base String for different barcodes are separated by space. Example: inDrop (Zilionis et al, Nat. Protocols, 2017): --solo_cb_position 0_0_2_-1 3_1_3_8
--solo_umi_position	string	position of the UMI on the barcode read, same as soloCBposition Example: inDrop (Zilionis et al, Nat. Protocols, 2017): --solo_cb_position 3_9_3_14
--solo_adapter_sequence	string	adapter sequence to anchor barcodes. Only one adapter sequence is allowed.
--solo_adapter_mismatches_nmax	integer	maximum number of mismatches allowed in adapter sequence.
--solo_cb_match_wl_type	string	matching the Cell Barcodes to the WhiteList - Exact ... only exact matches allowed - 1MM ... only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match. - 1MM_multi ... multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches. Allowed CBs have to have at least one read with exact match. This option matches best with CellRanger 2.2.0 - 1MM_multi_pseudocounts ... same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes. - 1MM_multi_Nbase_pseudocounts ... same as 1MM_multi_pseudocounts, multimatching to WL is allowed for CBs with N-bases. This option matches best with CellRanger >= 3.0.0 - EditDist_2 ... allow up to edit distance of 3 fpr each of the barcodes. May include one deletion + one insertion. Only works with --solo_type CB_UMI_Complex. Matches to multiple passlist barcdoes are not allowed. Similar to ParseBio Split-seq pipeline.
--solo_input_sam_attr_barcode_seq	string multiple	when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode sequence (in proper order). For instance, for 10X CellRanger or STARsolo BAMs, use --solo_input_sam_attr_barcode_seq CR UR . This parameter is required when running STARsolo with input from SAM.
--solo_input_sam_attr_barcode_qual	string multiple	when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode qualities (in proper order). For instance, for 10X CellRanger or STARsolo BAMs, use --solo_input_sam_attr_barcode_qual CY UY . If this parameter is '-' (default), the quality 'H' will be assigned to all bases.
--solo_strand	string	strandedness of the solo libraries: - Unstranded ... no strand information - Forward ... read strand same as the original RNA molecule - Reverse ... read strand opposite to the original RNA molecule
--solo_features	string multiple	genomic features for which the UMI counts per Cell Barcode are collected - Gene ... genes: reads match the gene transcript - SJ ... splice junctions: reported in SJ.out.tab - GeneFull ... full gene (pre-mRNA): count all reads overlapping genes' exons and introns - GeneFull_ExonOverIntron ... full gene (pre-mRNA): count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons - GeneFull_Ex50pAS ... full gene (pre-RNA): count all reads overlapping genes' exons and introns: prioritize >50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.
--solo_multi_mappers	string multiple	counting method for reads mapping to multiple genes - Unique ... count only reads that map to unique genes - Uniform ... uniformly distribute multi-genic UMIs to all genes - Rescue ... distribute UMIs proportionally to unique+uniform counts (~ first iteration of EM) - PropUnique ... distribute UMIs proportionally to unique mappers, if present, and uniformly if not. - EM ... multi-gene UMIs are distributed using Expectation Maximization algorithm
--solo_umi_dedup	string multiple	type of UMI deduplication (collapsing) algorithm - 1MM_All ... all UMIs with 1 mismatch distance to each other are collapsed (i.e. counted once). - 1MM_Directional_UMItools ... follows the "directional" method from the UMI-tools by Smith, Heger and Sudbery (Genome Research 2017). - 1MM_Directional ... same as 1MM_Directional_UMItools, but with more stringent criteria for duplicate UMIs - Exact ... only exactly matching UMIs are collapsed. - NoDedup ... no deduplication of UMIs, count all reads. - 1MM_CR ... CellRanger2-4 algorithm for 1MM UMI collapsing.
--solo_umi_filtering	string multiple	type of UMI filtering (for reads uniquely mapping to genes) - - ... basic filtering: remove UMIs with N and homopolymers (similar to CellRanger 2.2.0). - MultiGeneUMI ... basic + remove lower-count UMIs that map to more than one gene. - MultiGeneUMI_All ... basic + remove all UMIs that map to more than one gene. - MultiGeneUMI_CR ... basic + remove lower-count UMIs that map to more than one gene, matching CellRanger > 3.0.0 . Only works with --solo_umi_dedup 1MM_CR
--solo_out_file_names	string multiple	file names for STARsolo output: file_name_prefix gene_names barcode_sequences cell_feature_count_matrix
--solo_cell_filter	string multiple	cell filtering type and parameters - None ... do not output filtered cells - TopCells ... only report top cells by UMI count, followed by the exact number of cells - CellRanger2.2 ... simple filtering of CellRanger 2.2. Can be followed by numbers: number of expected cells, robust maximum percentile for UMI count, maximum to minimum ratio for UMI count The harcoded values are from CellRanger: nExpectedCells=3000; maxPercentile=0.99; maxMinRatio=10 - EmptyDrops_CR ... EmptyDrops filtering in CellRanger flavor. Please cite the original EmptyDrops paper: A.T.L Lun et al, Genome Biology, 20, 63 (2019): https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1662-y Can be followed by 10 numeric parameters: nExpectedCells maxPercentile maxMinRatio indMin indMax umiMin umiMinFracMedian candMaxN FDR simN The harcoded values are from CellRanger: 3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
--solo_out_format_features_gene_field3	string multiple	field 3 in the Gene features.tsv file. If "-", then no 3rd field is output.
--solo_cell_read_stats	string	Output reads statistics for each CB - Standard ... standard output

Name

Type & Properties

--solo_type

string

multiple

--solo_cb_type

string

--solo_cb_whitelist

string

multiple

--solo_cb_start

integer

--solo_cb_len

integer

--solo_umi_start

integer

--solo_umi_len

integer

--solo_barcode_read_length

integer

--solo_barcode_mate

integer

--solo_cb_position

string

multiple

--solo_umi_position

string

--solo_adapter_sequence

string

--solo_adapter_mismatches_nmax

integer

--solo_cb_match_wl_type

string

--solo_input_sam_attr_barcode_seq

string

multiple

--solo_input_sam_attr_barcode_qual

string

multiple

--solo_strand

string

--solo_features

string

multiple

--solo_multi_mappers

string

multiple

--solo_umi_dedup

string

multiple

--solo_umi_filtering

string

multiple

--solo_out_file_names

string

multiple

--solo_cell_filter

string

multiple

--solo_out_format_features_gene_field3

string

multiple

--solo_cell_read_stats

string

Inputs

Name	Type & Properties	Description
--input --readFilesIn	file required multiple	The single-end or paired-end R1 FastQ files to be processed.
--input_r2	file multiple	The paired-end R2 FastQ files to be processed. Only required if --input is a paired-end R1 file.

Name

Type & Properties

--input

--readFilesIn

file

required

multiple

--input_r2

file

multiple

Outputs

Name	Type & Properties	Description
--aligned_reads	file required output	The output file containing the aligned reads.
--reads_per_gene	file output	The output file containing the number of reads per gene.
--unmapped	file output	The output file containing the unmapped reads.
--unmapped_r2	file output	The output file containing the unmapped R2 reads.
--chimeric_junctions	file output	The output file containing the chimeric junctions.
--log	file output	The output file containing the log of the alignment process.
--splice_junctions	file output	The output file containing the splice junctions.
--reads_aligned_to_transcriptome	file output	The output file containing the alignments to transcriptome in BAM formats. This file is generated when --quantMode is set to TranscriptomeSAM.

Name

Type & Properties

--aligned_reads

file

required

output

--reads_per_gene

file

output

--unmapped

file

output

--unmapped_r2

file

output

--chimeric_junctions

file

output

--log

file

output

--splice_junctions

file

output

--reads_aligned_to_transcriptome

file

output