Question: htseq-count: error: the following arguments are required: featuresfilename
0
gravatar for sarfrajiiet
7 weeks ago by
sarfrajiiet0 wrote:
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

ADD COMMENTlink modified 9 days ago by h.mon25k • written 7 weeks ago by sarfrajiiet0
2
gravatar for swbarnes2
7 weeks ago by
swbarnes25.8k
United States
swbarnes25.8k wrote:

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

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by swbarnes25.8k

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 REPLYlink written 7 weeks ago by sarfrajiiet0

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 REPLYlink written 7 weeks ago by swbarnes25.8k

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 REPLYlink written 7 weeks ago by sarfrajiiet0

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

ADD REPLYlink written 7 weeks ago by swbarnes25.8k

i am using HG38 for alignment

ADD REPLYlink written 6 weeks ago by sarfrajiiet0
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