Run RNASeq analysis with reference genome based on the Tophat-Cufflinks pipeline
Usage:
---------------------------------------------------------------------------------------------------
Filename: Run_RNASeq_ref_pipe_v1.sh
Revision: 1.0
Date: 2018/10/24
Author: Wei Dong
Email: [email protected]
GitHub: https://github.com/Davey1220/
Description: This script was designed to conduct the RNASeq analysis with reference genome based on the Tophat-Cufflinks pipeline
---------------------------------------------------------------------------------------------------
Copyright: 2018 (c) Wei Dong
License: GPL
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License \
as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. \
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty \
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. \
If any changes are made to this script, please mail me a copy of the changes
---------------------------------------------------------------------------------------------------
Version 1.0 2018/10/24
# input.txt, list the sample name and clean reads in each line, seperated by tab or space
sample1 sample1_R1.fq.gz sample1_R2.fq.gz
sample2 sample2_R1.fq.gz sample2_R2.fq.gz
sample3 sample3_R1.fq.gz sample3_R3.fq.gz
OPTIONS:
-i input file, list the sample name and clean reads in each line, default input.txt
-g reference genome, default ref.genome.fasta
-G gtf/gff file with the reference genome, default ref.genome.gtf
-t thread, default 10
-h/? show help of this script
Example:
Run_RNASeq_ref_pipe_v1.sh -i input.txt -g ref.genome.fasta -G ref.genome.gtf -t 10