RNA-seq calling default setting

[gaow]

It implements the GTEx pipeline for GTEx / TOPMed project. Please refer to this page for detail. Except for Trimmomatic step, other steps follows from the GTEx pipeline.

Reference data

Reference hg fasta data is integrated with ERCC spike in sequence from https://tools.thermofisher.com/content/sfs/manuals/ERCC92.zip

Question: this is done by GTEx / TOPMed pipeline. Does it apply to the setting of a generic RNA-seq analysis?

Trimmomatic for adapter removal

      --fasta-with-adapters-etc 'TruSeq3-PE.fa'
                        Illumina clip setting Path to the reference adaptors
      --seed-mismatches 2 (as int)
      --palindrome-clip-threshold 30 (as int)
      --simple-clip-threshold 10 (as int)
      --window-size 4 (as int)
                        sliding window setting
      --required-quality 20 (as int)
      --leading 3 (as int)
                        Other settings
      --trailing 3 (as int)
      --min-len 50 (as int)

STAR

Question: does this apply to the setting of a generic RNA-seq analysis?

     --outFilterMultimapNmax 20 (as int)
                        Alignment parameter
      --alignSJoverhangMin 8 (as int)
      --alignSJDBoverhangMin 1 (as int)
      --outFilterMismatchNmax 999 (as int)
      --outFilterMismatchNoverLmax 0.1 (as float)
      --alignIntronMin 20 (as int)
      --alignIntronMax 1000000 (as int)
      --alignMatesGapMax 1000000 (as int)
      --outFilterType BySJout
      --outFilterScoreMinOverLread 0.33 (as float)
      --outFilterMatchNminOverLread 0.33 (as float)
      --limitSjdbInsertNsj 1200000 (as int)
      --outSAMstrandField intronMotif
      --outFilterIntronMotifs None
      --alignSoftClipAtReferenceEnds Yes
      --quantMode TranscriptomeSAM GeneCounts (as list)
      --outSAMattrRGline ID:rg1 SM:sm1 (as list)
      --outSAMattributes NH HI AS nM NM ch (as list)
      --chimSegmentMin 15 (as int)
      --chimJunctionOverhangMin 15 (as int)
      --chimOutType Junctions WithinBAM SoftClip (as list)
      --chimMainSegmentMultNmax 1 (as int)

RNA-SeQC 2

For gene-level TPM. Default to unstranded input data. Users must specify --stranded option for stranded input

RSEM

For isoform-level TPM. Default to unstranded input data. Users must specify --stranded option for stranded input. Other parameters:

  --max-frag-len 1000 (as int)
  --[no-]estimate-rspd (default to True)