Bash script to automate htseq-count

[gkuffel]

Hi everyone-

I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following error: "Please provide 2 arguments". Does anyone see something obvious I am missing:

#!/bin/bash

for samples in *.sam

do
gtf = "Galaxy135-\[Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.29.gtf\].gtf"
echo $sample
describer=$(echo ${sample} | sed 's/.sam//')
echo $describer

htseq-count -m union -r pos -i gene_name -a 10 ${describer}.sam $gtf > ${describer}.counts

done

[wdecoster]

I would advice using gnu parallel, with a command like this:

find . -name '*.bam' | parallel 'htseq-count -f bam -q -t gene -i gene_id {} pathtoyourgtf.gtf > {.}.counts'