README.md

Sequencing pipeline

Contains scripts for mRNA-Seq preprocessing

Dependencies

• RSeQC (version 4.0.0)
• STAR aligner (version 2.7.10a)
• HTSeq (version 2.0.2)

Usage

Rename raw sequencing files

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

Run mRNA-Seq pipeline

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

bash mRNA.preprocessing_master.sh -d {raw_directory}

arguments:  
d=[d]irectory with raw data (directory; required)  
g=reference [g]enome  
    accepted values: GRCh38, Mmul_10, Mnem_1  
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