htseq gene atrribute error

Question

[Balatheskulter]

$ htseq-count -q --additional-attr 534accepted_hits.bam 535accepted_hits.bam Rsolani.gff Error occured when processing GFF file (line 10 of file Rsolani.gff): Feature exon-AG1IA_00001-2 does not contain a 'gene_id' attribute [Exception type: ValueError, raised in count.py:79] what should I do now ?

Answer 1

[Strand NGS]

The gff3 file you are passing doesn't have the 'gene_id' attribute. Please do check the file and see the additional options in htseq to pass the correct id.

Some of other posts here that you can refer to:

htseq-count error Feature does not contain a 'gene_id' attribute

htseq-count error: "does not contain 'gene_id'

and many more are there available here to help.

[Balatheskulter]

please see this htseq coun error