Question: htseq-count: error: the following arguments are required: featuresfilename
0
gravatar for sarfrajiiet
13 months 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 11 months ago by h.mon29k • written 13 months ago by sarfrajiiet0
2
gravatar for swbarnes2
13 months ago by
swbarnes27.7k
United States
swbarnes27.7k wrote:

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

ADD COMMENTlink modified 13 months ago • written 13 months ago by swbarnes27.7k

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 13 months 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 13 months ago by swbarnes27.7k

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 13 months 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 13 months ago by swbarnes27.7k

i am using HG38 for alignment

ADD REPLYlink written 12 months ago by sarfrajiiet0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1540 users visited in the last hour