the results of featureCounts do not have `Geneid`

Question

[Francis]

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!

Answer 1

[EagleEye]

Hi,

It is not '-g --gene_id'. It should be '-g gene_id'.

[Francis]

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.

[EagleEye]

Can u post few lines of your GFF file?? Check whether you have gene_id feature type in 9th column of GTF/GFF file.

[Francis]

chr01   liftOver        gene    128254  129021  .       -       .       ID=YAL014C_BY4741;Name=YAL014C;orf_classification=Verified;gene=SYN8;Alias=SYN8,SLT2
chr01   liftOver        CDS     128254  129021  .       -       0       Parent=YAL014C_BY4741;Name=YAL014C_CDS;orf_classification=Verified
chr01   liftOver        gene    126905  128104  .       -       .       ID=YAL015C_BY4741;Name=YAL015C;orf_classification=Verified;gene=NTG1;Alias=NTG1,bifu
chr01   liftOver        CDS     126905  128104  .       -       0       Parent=YAL015C_BY4741;Name=YAL015C_CDS;orf_classification=Verified
chr01   liftOver        gene    124879  126786  .       +       .       ID=YAL016W_BY4741;Name=YAL016W;orf_classification=Verified;gene=TPD3;Alias=TPD3,FUN3
chr01   liftOver        CDS     124879  126786  .       +       0       Parent=YAL016W_BY4741;Name=YAL016W_CDS;orf_classification=Verified

And I try -g ID, it is wrong, too. So,...

Thanks.

[EagleEye]

Try replacing all 'ID=' to 'gene_id=' from your GFF and run again.