Bulk RNA-Sequencing pipeline

Contains scripts for bulk RNA-Seq preprocessing

Dependencies

• RSeQC (version 3.0.1)
• STAR aligner (version 2.7.0e)
• HTSeq (version 0.11.2)

Usage

Rename raw sequencing files

The pipeline expect raw sequencing files to be named using the convention SampleID_mate.fq.gz where:
SampleID can be any string
mate is the digit [1,2]
ex: S01_1.fq.gz

Run RNA-Seq pipeline

The RNA-Seq pipeline will map sequencing reads to a reference genome

bash rna.preprocessing_master.sh -d {raw_directory}

arguments:  
d=[d]irectory with raw data (directory; required)  
g=reference [g]enome  
    accepted values: GRCh38, GRCm39  
p=[p]air-end sequencing files  
    if arugment -p is not given, single-end sequencing files are  
    expected
e=[e]mail address  
i=[i]soform transcript/exon counts  
h=print [h]elp