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zeroes in ht-seq output

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)

rna-seq
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updated by Biostar Biostar • written by komal.yasmin • komal.yasmin

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

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written by Devon Ryan Devon Ryan

how do I confirm if they have different chromosome names?

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written by komal.yasmin • komal.yasmin 
cut -f 1 foo.gtf | sort | uniq -c
samtools view -H foo.bam
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written by Devon Ryan Devon Ryan

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