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Peppro QC PEP

Get source samples using geofetch

geofetch -i sra_accessions.txt -n ppqc

Grab the source sample metadata here:

wget -r http://big.databio.org/peppro/sra_meta/ppqc/ .

Get RNA-seq spike-in samples here:

wget http://big.databio.org/peppro/fastq/K562_[1-9]0pct_RNArc_r2.fastq.gz .

Validate the configuration file with eido like so:

eido -p peppro_paper.yaml -s http://schema.databio.org/pipelines/ProseqPEP.yaml

Create user-specific environment variables

  • $CODE: this is a path to the parent directory where scripts and code are stored
    • For example:CODE=/scratch/userid/src/
  • $DATA: this is a path to the parent directory where input files are stored
    • For example:DATA=/project/shefflab/data/
  • $PROCESSED: this is a path to the parent directory to where output should be written
    • For example:PROCESSED=/project/shefflab/processed/

Run in looper:

looper run ppqc/peppro_paper.yaml

The peppro_paper.yaml file is the working PEP for these samples. The peppro_paper.csv file is the working annotation file for these samples.

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QC samples for PEPPRO pipeline

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