rsem/rsem_prepare_reference

Transcriptome

Index

Description

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.

Type

bash_script

License

GPL-3.0

Keywords

Transcriptome

Index

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

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

Inputs

Name	Type & Properties	Description
--reference_fasta_files	file required multiple	Semi-colon separated list of Multi-FASTA formatted files OR a directory name. If a directory name is specified, RSEM will read all files with suffix ".fa" or ".fasta" in this directory. The files should contain either the sequences of transcripts or an entire genome, depending on whether the '--gtf' option is used.
--reference_name	string required	The name of the reference used. RSEM will generate several reference-related files that are prefixed by this name. This name can contain path information (e.g. '/ref/mm9').

Name

Type & Properties

--reference_fasta_files

file

required

multiple

--reference_name

string

required

Outputs

Name	Type & Properties	Description
--output	file required output	Directory containing reference files generated by RSEM.

Name

Type & Properties

--output

file

required

output

Other options

Name	Type & Properties	Description
--gtf	file	Assume that 'reference_fasta_files' contains the sequence of a genome, and extract transcript reference sequences using the gene annotations specified in the GTF file. If this and '--gff3' options are not provided, RSEM will assume 'reference_fasta_files' contains the reference transcripts. In this case, RSEM assumes that name of each sequence in the Multi-FASTA files is its transcript_id.
--gff3	file	GFF3 annotation file. Converted to GTF format with the file name 'reference_name.gtf'. Please make sure that 'reference_name.gtf' does not exist.
--gff3_rna_patterns	string multiple	List of transcript categories (separated by semi-colon). Only transcripts that match the string will be extracted.
--gff3_genes_as_transcripts	boolean_true	This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes. RSEM will assume each gene as a unique transcript when it converts the GFF3 file into GTF format.
--trusted_sources	string multiple	List of trusted sources (separated by semi-colon). Only transcripts coming from these sources will be extracted. If this option is off, all sources are accepted.
--transcript_to_gene_map	file	Use information from this file to map from transcript (isoform) ids to gene ids. Each line of this file should be of the form: gene_id transcript_id with the two fields separated by a tab character. If you are using a GTF file for the "UCSC Genes" gene set from the UCSC Genome Browser, then the "knownIsoforms.txt" file (obtained from the "Downloads" section of the UCSC Genome Browser site) is of this format. If this option is off, then the mapping of isoforms to genes depends on whether the '--gtf' option is specified. If '--gtf' is specified, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
--allele_to_gene_map	file	Use information from <file> to provide gene_id and transcript_id information for each allele-specific transcript. Each line of <file> should be of the form: gene_id transcript_id allele_id with the fields separated by a tab character. This option is designed for quantifying allele-specific expression. It is only valid if '--gtf' option is not specified. allele_id should be the sequence names presented in the Multi-FASTA-formatted files.
--polyA	boolean_true	Add poly(A) tails to the end of all reference isoforms. The length of poly(A) tail added is specified by '--polyA-length' option. STAR aligner users may not want to use this option.
--polyA_length	integer	The length of the poly(A) tails to be added.
--no_polyA_subset	file	Only meaningful if '--polyA' is specified. Do not add poly(A) tails to those transcripts listed in this file containing a list of transcript_ids.
--bowtie	boolean_true	Build Bowtie indices.
--bowtie2	boolean_true	Build Bowtie 2 indices.
--star	boolean_true	Build STAR indices.
--star_sjdboverhang	integer	Length of the genomic sequence around annotated junction. It is only used for STAR to build splice junctions database and not needed for Bowtie or Bowtie2. It will be passed as the --sjdbOverhang option to STAR. According to STAR's manual, its ideal value is max(ReadLength)-1, e.g. for 2x101 paired-end reads, the ideal value is 101-1=100. In most cases, the default value of 100 will work as well as the ideal value. (Default is 100)
--hisat2_hca	boolean_true	Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline.
--quiet -q	boolean_true	Suppress the output of logging information.

Name

Type & Properties

--gtf

file

--gff3

file

--gff3_rna_patterns

string

multiple

--gff3_genes_as_transcripts

boolean_true

--trusted_sources

string

multiple

--transcript_to_gene_map

file

--allele_to_gene_map

file

--polyA

boolean_true

--polyA_length

integer

--no_polyA_subset

file

--bowtie

boolean_true

--bowtie2

boolean_true

--star

boolean_true

--star_sjdboverhang

integer

--hisat2_hca

boolean_true

--quiet

-q

boolean_true

Prior-enhanced RSEM options

Name	Type & Properties	Description
--prep_pRSEM	boolean_true	A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms. The index files will be used for aligning ChIP-seq reads in prior-enhanced RSEM and the training set isoforms will be used for learning prior. A path to Bowtie executables and a mappability file in bigWig format are required when this option is on. Currently, Bowtie2 is not supported for prior-enhanced RSEM.
--mappability_bigwig_file	file	Full path to a whole-genome mappability file in bigWig format. This file is required for running prior-enhanced RSEM. It is used for selecting a training set of isoforms for prior-learning. This file can be either downloaded from UCSC Genome Browser or generated by GEM (Derrien et al., 2012, PLoS One).

Name

Type & Properties

--prep_pRSEM

boolean_true

--mappability_bigwig_file

file