rsem/rsem_calculate_expression

Transcriptome

Index

Alignment

RSEM

Description

Calculate expression with RSEM.

Input

Name	Type & Properties	Description
--id	string	Sample ID.
--strandedness	string	Sample strand-specificity. Must be one of unstranded, forward, reverse
--paired	boolean_true	Paired-end reads or not?
--input	file multiple	Input reads for quantification.
--index	file	RSEM index.
--extra_args	string	Extra rsem-calculate-expression arguments in addition to the examples.

Name

Type & Properties

--id

string

--strandedness

string

--paired

boolean_true

--input

file

multiple

--index

file

--extra_args

string

Output

Name	Type & Properties	Description
--counts_gene	file output	Expression counts on gene level
--counts_transcripts	file output	Expression counts on transcript level
--stat	file output	RSEM statistics
--logs	file output	RSEM logs
--bam_star	file output	BAM file generated by STAR (optional)
--bam_genome	file output	Genome BAM file (optional)
--bam_transcript	file output	Transcript BAM file (optional)
--sort_bam_by_read_name	boolean_true	Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce deterministic maximum likelihood estimations from independent runs. Note that sorting will take long time and lots of memory.
--no_bam_output	boolean_true	Do not output any BAM file.
--sampling_for_bam	boolean_true	When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0.
--output_genome_bam	boolean_true	Generate a BAM file, 'sample_name.genome.bam', with alignments mapped to genomic coordinates and annotated with their posterior probabilities. In addition, RSEM will call samtools (included in RSEM package) to sort and index the bam file. 'sample_name.genome.sorted.bam' and 'sample_name.genome.sorted.bam.bai' will be generated.
--sort_bam_by_coordinate	boolean_true	Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices.

Name

Type & Properties

--counts_gene

file

output

--counts_transcripts

file

output

--stat

file

output

--logs

file

output

--bam_star

file

output

--bam_genome

file

output

--bam_transcript

file

output

--sort_bam_by_read_name

boolean_true

--no_bam_output

boolean_true

--sampling_for_bam

boolean_true

--output_genome_bam

boolean_true

--sort_bam_by_coordinate

boolean_true

Basic Options

Name	Type & Properties	Description
--no_qualities	boolean_true	Input reads do not contain quality scores.
--alignments	boolean_true	Input file contains alignments in SAM/BAM/CRAM format. The exact file format will be determined automatically.
--fai	file	If the header section of input alignment file does not contain reference sequence information, this option should be turned on. <file> is a FAI format file containing each reference sequence's name and length. Please refer to the SAM official website for the details of FAI format.
--bowtie2	boolean_true	Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local and discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In particular, we use options '--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score_min L,0,-0.1' by default. The last parameter of '--score_min', '-0.1', is the negative of maximum mismatch rate. This rate can be set by option '--bowtie2_mismatch_rate'. If reads are paired-end, we additionally use options '--no_mixed' and '--no_discordant'.
--star	boolean_true	Use STAR to align reads. Alignment parameters are from ENCODE3's STAR-RSEM pipeline. To save computational time and memory resources, STAR's Output BAM file is unsorted. It is stored in RSEM's temporary directory with name as 'sample_name.bam'. Each STAR job will have its own private copy of the genome in memory.
--hisat2_hca	boolean_true	Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast.
--append_names	boolean_true	If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated by '_') in files 'sample_name.isoforms.results' and 'sample_name.genes.results'.
--seed	integer	Set the seed for the random number generators used in calculating posterior mean estimates and credibility intervals. The seed must be a non-negative 32 bit integer.
--single_cell_prior	boolean_true	By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility intervals. However, much less genes are expressed in single cell RNA-Seq data. Thus, if you want to compute posterior mean estimates and/or credibility intervals and you have single-cell RNA-Seq data, you are recommended to turn on this option. Then RSEM will use Dirichlet(0.1) as the prior which encourage the sparsity of the expression levels.
--calc_pme	boolean_true	Run RSEM's collapsed Gibbs sampler to calculate posterior mean estimates.
--calc_ci	boolean_true	Calculate 95% credibility intervals and posterior mean estimates. The credibility level can be changed by setting '--ci_credibility_level'.
--quiet -q	boolean_true	Suppress the output of logging information.

Name

Type & Properties

--no_qualities

boolean_true

--alignments

boolean_true

--fai

file

--bowtie2

boolean_true

--star

boolean_true

--hisat2_hca

boolean_true

--append_names

boolean_true

--seed

integer

--single_cell_prior

boolean_true

--calc_pme

boolean_true

--calc_ci

boolean_true

--quiet

-q

boolean_true

Aligner Options

Name	Type & Properties	Description
--seed_length	integer	Seed length used by the read aligner. Providing the correct value is important for RSEM. If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter. Any read with its or at least one of its mates' (for paired-end reads) length less than this value will be ignored. If the references are not added poly(A) tails, the minimum allowed value is 5, otherwise, the minimum allowed value is 25. Note that this script will only check if the value >= 5 and give a warning message if the value < 25 but >= 5. (Default: 25)
--phred64_quals	boolean_true	Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. >= 1.3). This option is used by Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)
--solexa_quals	boolean_true	Input quality scores are solexa encoded (from GA Pipeline ver. < 1.3). This option is used by Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)
--bowtie_n	integer	(Bowtie parameter) max # of mismatches in the seed. (Range: 0-3, Default: 2)
--bowtie_e	integer	(Bowtie parameter) max sum of mismatch quality scores across the alignment. (Default: 99999999)
--bowtie_m	integer	(Bowtie parameter) suppress all alignments for a read if > <int> valid alignments exist. (Default: 200)
--bowtie_chunkmbs	integer	(Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use Bowtie's default)
--bowtie2_mismatch_rate	double	(Bowtie 2 parameter) The maximum mismatch rate allowed. (Default: 0.1)
--bowtie2_k	integer	(Bowtie 2 parameter) Find up to <int> alignments per read. (Default: 200)
--bowtie2_sensitivity_level	string	(Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end mode. This option controls how hard Bowtie 2 tries to find alignments. <string> must be one of "very_fast", "fast", "sensitive" and "very_sensitive". The four candidates correspond to Bowtie 2's "--very-fast", "--fast", "--sensitive" and "--very-sensitive" options. (Default: "sensitive" - use Bowtie 2's default)
--star_gzipped_read_file	boolean_true	Input read file(s) is compressed by gzip. (Default: false)
--star_bzipped_read_file	boolean_true	Input read file(s) is compressed by bzip2. (Default: false)
--star_output_genome_bam	boolean_true	Save the BAM file from STAR alignment under genomic coordinate to 'sample_name.STAR.genome.bam'. This file is NOT sorted by genomic coordinate. In this file, according to STAR's manual, 'paired ends of an alignment are always adjacent, and multiple alignments of a read are adjacent as well'. (Default: false)

Name

Type & Properties

--seed_length

integer

--phred64_quals

boolean_true

--solexa_quals

boolean_true

--bowtie_n

integer

--bowtie_e

integer

--bowtie_m

integer

--bowtie_chunkmbs

integer

--bowtie2_mismatch_rate

double

--bowtie2_k

integer

--bowtie2_sensitivity_level

string

--star_gzipped_read_file

boolean_true

--star_bzipped_read_file

boolean_true

--star_output_genome_bam

boolean_true

Advanced Options

Name	Type & Properties	Description
--tag	string	The name of the optional field used in the SAM input for identifying a read with too many valid alignments. The field should have the format <tagName>:i:<value>, where a <value> bigger than 0 indicates a read with too many alignments. (Default: "")
--fragment_length_min	integer	Minimum read/insert length allowed. This is also the value for the Bowtie/Bowtie2 -I option. (Default: 1)
--fragment_length_max	integer	Maximum read/insert length allowed. This is also the value for the Bowtie/Bowtie 2 -X option. (Default: 1000)
--fragment_length_mean	integer	(single-end data only) The mean of the fragment length distribution, which is assumed to be a Gaussian. (Default: -1, which disables use of the fragment length distribution)
--gragment_length_sd	double	(single-end data only) The standard deviation of the fragment length distribution, which is assumed to be a Gaussian. (Default: 0, which assumes that all fragments are of the same length, given by the rounded value of --fragment_length_mean).
--estimate_rspd	boolean_true	Set this option if you want to estimate the read start position distribution (RSPD) from data. Otherwise, RSEM will use a uniform RSPD.
--num_rspd_bins	integer	Number of bins in the RSPD. Only relevant when '--estimate_rspd' is specified. Use of the default setting is recommended. (Default: 20)
--gibbs_burnin	integer	The number of burn-in rounds for RSEM's Gibbs sampler. Each round passes over the entire data set once. If RSEM can use multiple threads, multiple Gibbs samplers will start at the same time and all samplers share the same burn-in number. (Default: 200)
--gibbs_number_of_samples	integer	The total number of count vectors RSEM will collect from its Gibbs samplers. (Default: 1000)
--gibbs_sampling_gap	integer	The number of rounds between two succinct count vectors RSEM collects. If the count vector after round N is collected, the count vector after round N + <int> will also be collected. (Default: 1)
--ci_credibility_level	double	The credibility level for credibility intervals. (Default: 0.95)
--ci_number_of_samples_per_count_vector	integer	The number of read generating probability vectors sampled per sampled count vector. The crebility intervals are calculated by first sampling P(C \| D) and then sampling P(Theta \| C) for each sampled count vector. This option controls how many Theta vectors are sampled per sampled count vector. (Default: 50)
--keep_intermediate_files	boolean_true	Keep temporary files generated by RSEM. RSEM creates a temporary directory, 'sample_name.temp', into which it puts all intermediate output files. If this directory already exists, RSEM overwrites all files generated by previous RSEM runs inside of it. By default, after RSEM finishes, the temporary directory is deleted. Set this option to prevent the deletion of this directory and the intermediate files inside of it.
--temporary_folder	string	Set where to put the temporary files generated by RSEM. If the folder specified does not exist, RSEM will try to create it. (Default: sample_name.temp)
--time	boolean_true	Output time consumed by each step of RSEM to 'sample_name.time'.

Name

Type & Properties

--tag

string

--fragment_length_min

integer

--fragment_length_max

integer

--fragment_length_mean

integer

--gragment_length_sd

double

--estimate_rspd

boolean_true

--num_rspd_bins

integer

--gibbs_burnin

integer

--gibbs_number_of_samples

integer

--gibbs_sampling_gap

integer

--ci_credibility_level

double

--ci_number_of_samples_per_count_vector

integer

--keep_intermediate_files

boolean_true

--temporary_folder

string

--time

boolean_true

Prior-Enhanced RSEM Options

Name	Type & Properties	Description
--run_pRSEM	boolean_true	Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e. isoform's initial pseudo-count for RSEM's Gibbs sampling, will be learned from input RNA-seq data and an external data set. When pRSEM needs and only needs ChIP-seq peak information to partition isoforms (e.g. in pRSEM's default partition model), either ChIP-seq peak file (with the '--chipseq_peak_file' option) or ChIP-seq FASTQ files for target and input and the path for Bowtie executables are required (with the '--chipseq_target_read_files <string>', '--chipseq_control_read_files <string>', and '--bowtie_path <path> options), otherwise, ChIP-seq FASTQ files for target and control and the path to Bowtie executables are required.
--chipseq_peak_file	file	Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e. BED6+4, format. This file is used when running prior-enhanced RSEM in the default two-partition model. It partitions isoforms by whether they have ChIP-seq overlapping with their transcription start site region or not. Each partition will have its own prior parameter learned from a training set. This file can be either gzipped or ungzipped.
--chipseq_target_read_files	file	Comma-separated full path of FASTQ read file(s) for ChIP-seq target. This option is used when running prior-enhanced RSEM. It provides information to calculate ChIP-seq peaks and signals. The file(s) can be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options '--bowtie_path <path>' and '--chipseq_control_read_files <string>' must be defined when this option is specified.
--chipseq_control_read_files	file	Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol. This option is used when running prior-enhanced RSEM. It provides information to call ChIP-seq peaks. The file(s) can be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options '--bowtie_path <path>' and '--chipseq_target_read_files <string>' must be defined when this option is specified.
--chipseq_read_files_multi_targets	file	Comma-separated full path of FASTQ read files for multiple ChIP-seq targets. This option is used when running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. It provides information to calculate ChIP-seq signals. All files can be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. When this option is specified, the option '--bowtie_path <path>' must be defined and the option '--partition_model <string>' will be set to 'cmb_lgt' automatically.
--chipseq_bed_files_multi_targets	file	Comma-separated full path of BED files for multiple ChIP-seq targets. This option is used when running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. It provides information of ChIP-seq signals and must have at least the first six BED columns. All files can be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. When this option is specified, the option '--partition_model <string>' will be set to 'cmb_lgt' automatically.
--cap_stacked_chipseq_reads	boolean_true	Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval. This option is used when running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. This option is only in use when either '--chipseq_read_files_multi_targets <string>' or '--chipseq_bed_files_multi_targets <string>' is specified.
--n_max_stacked_chipseq_reads	integer	The maximum number of stacked ChIP-seq reads to keep. This option is used when running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. This option is only in use when the option '--cap_stacked_chipseq_reads' is set.
--partition_model	string	A keyword to specify the partition model used by prior-enhanced RSEM. It must be one of the following keywords: * pk * pk_lgtnopk * lm3, lm4, lm5, or lm6 * nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk * pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk * cmb_lgt Parameters for all the above models are learned from a training set. For detailed explanations, please see prior-enhanced RSEM's paper. (Default: 'pk')

Name

Type & Properties

--run_pRSEM

boolean_true

--chipseq_peak_file

file

--chipseq_target_read_files

file

--chipseq_control_read_files

file

--chipseq_read_files_multi_targets

file

--chipseq_bed_files_multi_targets

file

--cap_stacked_chipseq_reads

boolean_true

--n_max_stacked_chipseq_reads

integer

--partition_model

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
counts_gene: "$id.$key.counts_gene.results"  
counts_transcripts: "$id.$key.counts_transcripts.results"  
stat: "$id.$key.stat.stat"  
logs: "$id.$key.logs.log"  
bam_star: "$id.$key.bam_star.bam"  
bam_genome: "$id.$key.bam_genome.bam"  
bam_transcript: "$id.$key.bam_transcript.bam"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/rsem/rsem_calculate_expression/main.nf \  
  -params-file params.yaml

rsem/rsem_calculate_expression

Input

Output

Basic Options

Aligner Options

Advanced Options

Prior-Enhanced RSEM Options

Run this component

Relationships

Used by

Uses