extract_protein_coding_lincRNA_genes.sh

#!/bin/bash
#SBATCH --time 20:00:00
#SBATCH --no-requeue
#SBATCH --nodes=1
#SBATCH --ntasks=6
#SBATCH -p shared



### Extract protein-coding genes and lincRNA from the TPM gene matrix

datadir=./GTEx_data/
cd  ${datadir}
GENCODE="gencode.v26.annotation.gene.txt"

cat $GENCODE | grep protein_coding  | awk '{print $1}'  | uniq  >> pc.lc.genes
cat $GENCODE  | grep lincRNA | awk '{print $1}'  | uniq  >> pc.lc.genes

sort pc.lc.genes > temp
mv temp pc.lc.genes

split -l 5000 GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct  
for fn in x*
do
	grep -w -F -f pc.lc.genes ${fn} > ${fn}.pc.lc
done

grep -m1 "Description" GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct  > gene_pc_lc_tpm.txt
cat x*pc.lc >> gene_pc_lc_tpm.txt

rm x*