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htseq-count: error: the following arguments are required: featuresfilename
htseq-count -f bam -r name -i gene_id -s no -t exon /Users/abc/sorted.bam > count.txt

usage: htseq-count [options] alignment_file gff_file
htseq-count: error: the following arguments are required: featuresfilename

not getting what's wrong in my code help me

rna-seq rna-seq alignment sequencing sequence
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updated by h.mon h.mon • written by sarfrajiiet • sarfrajiiet

1 answer

You give the software no gff. How is it supposed to assign reads to genes without one?

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written by swbarnes2 swbarnes2

Thank you for your reply I have human rna sequence( paired ) so from where I get this gff file for this and then what the command I have to follow

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written by sarfrajiiet • sarfrajiiet

Get your gtf from the sample place that the genome you aligned to came from. I don't know where you are getting your references, you have to know that.

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written by swbarnes2 swbarnes2

I'm not sure HTseq-count takes gff3 format, but the best way to find out is to try it.

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written by swbarnes2 swbarnes2

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