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D3B_RMATS.md

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D3b rMATS Workflow

Introduction

The rMATS workflow can also be run as a standalone workflow. In this workflow, rMATS is run on the input BAM files to generate 5 junction files: [alternative_3_prime_splice_sites_jc, alternative_5_prime_splice_sites_jc, mutually_exclusive_exons_jc, retained_introns_jc, skipped_exons_jc]. The workflow next grabs the sample information from the sample_1_bams by parsing the read group information from the BAM header for use in the output names. Each of the five junction files then undergo a simple filtering process where calls that have junction counts less than 10 are removed. These filtered junction files are returned as the final outputs.

Usage

Inputs

  • gtf_annotation: Input gtf annotation file
  • sample_1_bams:: Input sample 1 bam files
  • sample_2_bams:: Input sample 2 bam files
  • read_length:: Input read length for sample reads
  • variable_read_length: Allow reads with lengths that differ from --readLength to be processed. --readLength will still be used to determine IncFormLen and SkipFormLen
  • read_type: Select one option for input read type either paired or single. Tool default: paired
  • strandedness: Select one option for input strandedness. Tool default: fr-unstranded
  • novel_splice_sites:: Select for novel splice site detection or unannotated splice sites. 'true' to detect or add this parameter, 'false' to disable denovo detection. Tool Default: false
  • stat_off:: Select to skip statistical analysis, either between two groups or on single sample group. 'true' to add this parameter. Tool default: false
  • allow_clipping:: Allow alignments with soft or hard clipping to be used
  • output_basename:: String to use as basename for output files
  • rmats_threads:: Threads to allocate to RMATs
  • rmats_ram:: GB of RAM to allocate to RMATs

Outputs

  • filtered_alternative_3_prime_splice_sites_jc: File extension filtered.A3SS.MATS.JC.txt. Alternative 3 prime splice sites JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support
  • filtered_alternative_5_prime_splice_sites_jc: File extension filtered.A5SS.MATS.JC.txt. Alternative 5 prime splice sites JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support
  • filtered_mutually_exclusive_exons_jc: File extension filtered.MXE.MATS.JC.txt. Mutually exclusive exons JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support
  • filtered_retained_introns_jc: File extension filtered.RI.MATS.JC.txt. Retained introns JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support
  • filtered_skipped_exons_jc: File extension filtered.SE.MATS.JC.txt. Skipped exons JC.txt output from RMATs containing only those calls with 10 or more junction spanning read counts of support