Entering edit mode
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
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
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.
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
I'm not sure HTseq-count takes gff3 format, but the best way to find out is to try it.
i am using HG38 for alignment