Wrapper for DEXseq read counting

dexseq_count_em.sh

#!/bin/bash
samdir="./"
dexseq_flat_gff="my.DEXSeq.gff"
outdir="./dexseq-count"
dexseq_count="python /home/foo/bin/dexseq_count.py"
samtools=`which samtools`

if ! [ -d "$outdir" ];
then
        mkdir -p $outdir
fi


for BAM in $(ls $samdir/*.bam)
do
bn=$(basename $BAM .uniq.bam)
echo "processing" $bn.uniq.bam
set -x
$samtools sort -n -o $BAM $bn | $samtools view -h - | $dexseq_count -p yes -s no -r pos -f sam $dexseq_flat_gff - $outdir/$bn.dexseq.count 2> $outdir/$bn.dexseq.count.err
set +x
done