htseq-count no result give me
hi all
i have work with htseq-count. but no give output for me.
yghb@yghb-virtual-machine:~/amraei/count$ htseq-count -f bam ~/amraei/bam-file/A1.bam ~/amraei/gene/Zea_mays.B73_RefGen_v4.42.gtf > A1-count.txt
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yaghoub.amraei •
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yaghoub.amraei •
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No results meaning blank file or no features?
No results meaning blank file
Any error messages? Can you post some lines from the gtf file and the bam file?
enter link description here
Not a link... Post some lines.
fix question me... thanks Asef
Do chromosome identifiers in your gtf and alignment files match? That would be the first thing to check.