#!/bin/bash
#PBS -q hotel
#PBS -N s10_featurecounts
#PBS -l nodes=1:ppn=8
#PBS -l walltime=0:30:00
#PBS -o s10_featurecounts_out.o
#PBS -e s10_featurecounts_error.e
#PBS -V
#PBS -M t2shaw@ucsd.edu
#PBS -m abe

featureCounts -T 8 \
    -s -B --primary \
    -a /projects/ps-yeolab/biom262-2016/genomes/mm10/gencode/m8/gencode.vM8.bas$
    -o ~/projects/shalek2013/processed_data/s10_featureCounts.txt \
    ~/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam