/bdsRNAseqPipeline

RNA-seq pipeline for raw (fastq) file alignment, (if) trimming, (if) count and some other good stuff

This is documentation for rnas-pipe BDS script located in this sub-repository

RNA-seq(uencing) a.k.a Whole-transcriptome sequencing

First files biologist ever encounter from the sequencing facility are FASTQ files. These are really your raw data. The rnas-pipe allows you easily submit your fastq directory for read alignment. On top of that you can also get fastqc and RNA-SeQC reports and reads count for all of your bam files.

Caveats

  • at the moment only can run STAR mapper with fixed options
  • right now -fastqDir parameter will only work with . i.e your execute rnas-pipe in the directory where your fastq files are
  • prePro is a must if you want to gete RNA-SeQC report
  • at the moment there isn't an option to choose the strand direction for read counts right now rnas-pipe simply counts all bams against stranded NO and stranded REVERSE options

The rnas-pipe features:

  1. Reads alignment. Currently it is set to STAR with predefined STAR input parameters It is rather stringent at this stage and only through manual intervention one can change the input parameters inside the source code. Feel free to git clone and edit source to your needs. There are the parameters STAR set up to run with in BDS by default.

    STAR --runThreadN 26 \
     --genomeDir $genomeIndex \
     --outSAMtype BAM Unsorted \
     --outSAMattrRGline ID:$laneNumber CN:AGRF DS:RNA-seq PL:ILLUMINA PM:MiSeq SM:$uniqueName \
     --outSAMunmapped Within \
     --readFilesCommand zcat \
     --readFilesIn $read1 $read2 \
     --outFileNamePrefix $preFix

  2. Several picard pre-processing steps for RNA-SeQC run later. picard produces, sorted, reordered bam files with marked duplicates. This is prerequisite for RNA-SeQC run

  3. featureCouunts that count how many reads mapped one genes

Work in progress

I'm working on including fastqc report at the first item to run in the pipeline