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README_CRG.md

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Specific README for CRG

Install

Singularity is already installed. You need to add to log to nextflow node:

ssh -Y nextflow.linux.crg.es

Then change your .bashrc file for adding the right version of singularity:

vi $HOME/.bashrc

type i for inserting and copy paste this:

module use /software/as/el7.2/EasyBuild/CRG/modules/all
module load Singularity/3.2.1

and exit typing:

:wq

and return.

Then you can clone the repository:

git clone --depth 1 git@github.com:biocorecrg/allele_specific_RNAseq.git

or

git clone --depth 1 https://github.com/biocorecrg/allele_specific_RNAseq.git

depending on your GitHub configuration.

Annotation data

Annotation data are available at:

/users/bpayer/sequencing_analysis/pipe_data

You have:

  • SNPs annotations: CAST_EiJ-129S1_SvImJ.vcf.gz
  • Mouse reference genome: Mus_musculus.GRCm38.68.dna.chrom.fa.gz
  • Mouse annotation: Mus_musculus.GRCm38.68.gtf.gz

The parameters for running the pipeline are defined in the file params.crg.config. You can copy this file and renaming it params.config and change it accordingly.

In particular you need to change only the following parameters:

	reads        = "/test/*_{1,2}.fastq.gz"
	strandness   = "reverse"
  output       = "$baseDir/output_test"
	single       = "NO"
	varcut       = 1
  title	     = "Allele specific RNAseq project"	
	subtitle     = "This is my wonderful RNA experiment"	
	PI           = "Luca Cozzuto"	
	User	     = "Luca Cozzuto"
	email	     = "mymail@mydomain.eu"