STARlight

RNA-seq STAR Pipeline

How to run:

Load the required modules:

module load snakemake-7.12.1 STAR-2.7.10a subread-2.0.1 picard-2.23.8 fastqc-0.11.9 R-4.0.3 multiqc-1.9 cutadapt-3.3 samtools-1.11 deeptools-3.5.0

Run the Snakemake command pointing to the location of the .smk file and the config file:

snakemake -p --cores 12 -s /path/to/STARlight/STARlight.smk --configfile /path/to/config.json

If you need to merge fastq files coming from different lanes you can run catlanes ahead of STARlight:

module load snakemake-7.12.1 fastqc-0.11.9 multiqc-1.9
snakemake -p 12 -s catlanes.smk --configfile /path/to/catlanes.json

Important files:

In order to run the pipeline you need to modify the config file accordingly to your input files. Moreover, you need to provide a file containing the sample information and a table of comparisons to perform.

sampleInfo file example:

name	condition
1_S1	CTR
2_S2	LNO
3_S3	HNO
4_S4	CTR
5_S5	LNO
6_S6	HNO

compsTab file example:

comp	cond1	cond2
LNO_vs_CTR	LNO	CTR
HNO_vs_CTR	HNO	CTR
HNO_vs_LNO	HNO	LNO

How to select the species:

STARlight works with ENSEMBL. A reference genome and a GTF file for the interested species are needed and could be downloaded via FTP. The config file should be modified to point the right path to these files. The pipeline is using BioMart for the complete annotation so you have to specify the correct species in the config file. The species supported are listed in STARlight/biomaRt/listDatasets.biomaRt.txt. For example:

human: hsapiens_gene_ensembl
mouse: mmusculus_gene_ensembl