Hello, I'm trying to count the gene abundance from Metagenomic libraries using htseq-count program
from blast otuput format table 6 I converted it into a gff file with blast2gff, after that I used gat program
agat_convert_sp_gff2gtf.pl to convert the gff to gtf. This is how the gtf file looks like:
and this is how one of the htseq-count output table looks like using a bam file
It seem something is missing on the gtf table but I cannot figure out what is lacking, this is the code that I used:
So why it outputs "0" values of counts ? even the first column of the htseq-count program provide "nbisL1" names that I don't know to what they refer to.
Hello, I'm trying to count the gene abundance from Metagenomic libraries using
htseq-count programfrom blast otuput format table 6 I converted it into a gff file withblast2gff, after that I used gat programagat_convert_sp_gff2gtf.plto convert the gff to gtf. This is how the gtf file looks like:and this is how one of the
htseq-countoutput table looks like using a bam fileIt seem something is missing on the gtf table but I cannot figure out what is lacking, this is the code that I used:
htseq-count -r pos -n 9 -t match_part -f bam sample1.bam sample_1.gtf > sample1_genes.countSo why it outputs "0" values of counts ? even the first column of the
htseq-countprogram provide "nbisL1" names that I don't know to what they refer to.Thanks for your time :)
Bests,
Valentín.