ExpressionPrediction/script at master · DoryAbelman/ExpressionPrediction · GitHub

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#!/bin/bash
#
#$ -cwd

#Script for inferring DNA expression

module load python2/2.7.15
module load R/3.6.1
module load samtools/1.9
python /mnt/work1/users/pughlab/projects/IEG_MiSEQ/Inferring_DNA_Expression/ExpressionPrediction-master/expression_prediction.py \
    -fq /mnt/work1/users/pughlab/projects/IEG_MiSEQ/fastq_links/MMRF.fastq.gz \
    -s Test_DuplicatesRemoved -g m -o /mnt/work1/users/pughlab/projects/IEG_MiSEQ/Inferring_DNA_Expression  \
    -k -t 20 -cna /mnt/work1/users/pughlab/projects/MMRF/WGS_analysis/ichorCNA/MMRF.seg \
    -tmp /mnt/work1/users/pughlab/projects/IEG_MiSEQ/Inferring_DNA_Expression/Temp \
    -step 5