Question

htseq-count: error: the following arguments are required: featuresfilename

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5.0 years ago

sarfrajiiet • 0

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 • 4.9k views

ADD COMMENT • link updated 4.9 years ago by h.mon 35k • written 5.0 years ago by sarfrajiiet • 0

score 2 · Accepted Answer · 2019-04-25

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5.0 years ago

swbarnes2 14k

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

ADD COMMENT • link 5.0 years ago by swbarnes2 14k

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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

ADD REPLY • link 5.0 years ago by sarfrajiiet • 0

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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.

ADD REPLY • link 5.0 years ago by swbarnes2 14k

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ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.long_noncoding_RNAs.gff3.gz

I AM USING THIS IS CORRECT

ADD REPLY • link 5.0 years ago by sarfrajiiet • 0

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