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README_CRG.md

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Specific README for CRG

Clone the repository:

git clone --depth 1 [email protected]:biocorecrg/allele_specific_RNAseq.git

or

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

depending on your GitHub configuration.

Install New CRG cluster

Singularity is already installed. You need to install nextflow locally and add to the path.

curl -s https://get.nextflow.io | bash
chmod +x nextflow
mkdir -p $HOME/.local/bin/
mv nextflow $HOME/.local/bin/

Then change your .bashrc file for adding the right version of JAVA and nextflow

vi $HOME/.bashrc

type i for inserting and copy paste this:

  
  export EASYBUILD_PREFIX=/software/sit/EasyBuild
  module use $EASYBUILD_PREFIX/modules/all
  module load Java/11.0.20
  export PATH=$HOME/.local/bin/:$PATH

and exit typing:

:wq

and return.

For launching the pipeline you need to create a folder in /scratch or /nfs/scratch02 and then pass this via command line:

mkdir /scratch/YOURGROUP/workdir

sbatch launch_nf.sh nextflow run as_rnaseq.nf -with-singularity -ansi-log false -profile slurm -w /scratch/YOURGROUP/workdir

Install (OLD CLUSTER)

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.

For launching the pipeline you need to create a folder in /nfs/scratch

mkdir /scratch/YOURGROUP/workdir

nextflow run as_rnaseq.nf -with-singularity -bg -w /scratch/YOURGROUP/workdir > log.txt

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	     = "[email protected]"