by Judith Bergadà Pijuan
This RNAseq pipeline is a tool to perform end-to-end RNAseq analyses. Given sequencing reads (FASTQ files), it provides a list of differentially expressed genes across conditions.
To use this pipeline, you need to install the following dependencies:
- STAR >= 2.7.3a
- FastQC >= v0.11.9
- R >= 3.6.0
Later, you need to download the tool:
cd $HOME
git clone https://github.com/judithbergada/Pipeline_RNAseqThe pipeline expects you to have the following folders:
- FASTQ folder: this is a folder containing only your sequencing reads (FASTQ files).
- Annotation folder: this is a folder containing only 2 files (a FASTA file and a GTF file).
In addition, you will need at least one text file showing the experimental design. It should look as follows:
Rep1_3_S24_R1_001 ctrl
Rep2_3_S31_R1_001 ctrl
Rep3_3_S38_R1_001 ctrl
Rep1_4_S25_R1_001 experiment
Rep2_4_S32_R1_001 experiment
Rep3_4_S39_R1_001 experiment
To get information about the usage, please try:
./RNAseq.sh -hThe RNAseq tool can be used with these parameters:
Usage: RNAseq [-h or --help]
[-f or --fastqfolder]
[-a or --annotfolder]
[-c or --condfiles]
[-r or --revfastqfolder]
[-o or --outname]
[-t or --threads]
Optional arguments:
-h, --help:
Show this help message and exit.
-o, --outname:
Name of your analysis.
It will be used to name the output files.
Default: rnaseq.
-t, --threads:
Number of threads that will be used.
It must be an integer.
Default: 8.
-r, --revfastqfolder:
If you are using paired-end reads, this should be the
path to the folder that contains ALL your REVERSE reads.
Only FASTQ files should be placed in it.
Files might (or might not) be compressed.
Note: ONLY REVERSE reads must be found in this folder, and
we recommend to name the files exactly as the forward reads but
adding _2 or _reverse at the end (followed by .fastq or .fq.gz).
Required arguments:
-f, --fastqfolder:
Path to the folder that contains ALL your FASTQ files.
Only FASTQ files should be placed in it.
Files might (or might not) be compressed.
Note: if you are using paired-end reads, this should be the
folder that contains ONLY your FORWARD reads.
-a, --annotfolder:
Path to the folder that contains the annotation files.
Only 2 files should be placed in this folder:
1) Whole genome FASTA file, 2) GTF file.
-c, --condfiles:
Path to a tab-delimited text file describing the
experimental design or comparisons. 2 columns are needed:
Column 1: name of each FASTQ file, without extension.
Column 2: condition of each file (experiment or control).
You can specify as many files as you want, but
they must be writen within quotes.
E.g.: --condfiles 'comparison1.txt comparison2.txt'
Enjoy using the tool!