zeroes in ht-seq output

Question

[komal.yasmin]

I am using ht seq to analyse RNA- seq data for Drosophila. I have used GFF3 file as well as GTF file in the script. I do not get an error report but the output file generated only contains gene IDs against zeroes for feature counts . Can someone please tell me what am I doing wrong? I am using the following script:

htseq-count --order=name --type=gene --idattr=ID --stranded=no --mode=union $ALIGNMENT_FILE $GFF_FILE > $EXPRESSION (Idattr is ID for Gff file and gene_id for gtf file)

[Devon Ryan]

Odds are good that your GTF and BAM file have different chromosome names.

[komal.yasmin]

how do I confirm if they have different chromosome names?

[Devon Ryan]

cut -f 1 foo.gtf | sort | uniq -c
samtools view -H foo.bam