Entering edit mode
6.9 years ago
Francis
▴
20
Hi,
I am doing some RNA-seq analysis of Yeast, there are some questions in counting reads(with featureCounts). I find the Yeast GFF file include genes and CDS, most are same. -a
use Yeast.gff
, and the result is below:
Geneid Chr Start End Strand Length C2_1.sam
chr07;chr07;***;chr17 73829;110625;***;78091 73902;110696;***;78164 -;-;***;+;- 65781 13195
there are no Geneid, i use the parameter -g --gene_id
in featureCounts.
so i don`t know the question is in annotation file Yeast.gff
or featureCounts` parameters.
Thanks!
Oh, I am sorry.
I used the parameter is
-g gene_id
, but there are not Geneid in output files. I want to select the raw of 'gene' in gff file as the annotation file not include 'CDS' raw. But i do not think it`s a good idea.I had done human RNA-seq and used featureCounts to count reads, the same parameters, no error. So it is a terrible question.
I suspect the the problem is gff file. But I do not search the example of Yeast to count reads or similarity solution.
Can u post few lines of your GFF file?? Check whether you have gene_id feature type in 9th column of GTF/GFF file.
And I try
-g ID
, it is wrong, too. So,...Thanks.
Try replacing all 'ID=' to 'gene_id=' from your GFF and run again.