HT-Seq, Gene ID appeared in Gene Name row

Question

[TM]

Hi, I am doing alignment with HISAT2 and couting with HT-seq. I got the counting matrix but i found there are gene ID appear in the gene name row. Is it normal that gene ID can appear like this or are there any problems regarding the counting step? Please help me, thank you in advance!

[abedkurdi10]

while running ht-seq, by default -i option is gene_id. use -i gene_name, this will assign gene names instead of gene ids.

[TM]

The following is my script: python3 -m HTSeq.scripts.count -f bam -r pos -m union -s reverse -t exon -i gene_id \ --additional-attr=gene_name \

So I need to change -i gene_id -> -i gene_name, how about the additional-attr, is it remain gene_name the same?

[Istvan Albert]

check your file that you used to specify the annotations, investigate the attributes for the transcripts in question

[TM]

Can you help me check my script? I am quite beginner in HT-seq. python3 -m HTSeq.scripts.count -f bam -r pos -m union -s reverse -t exon -i gene_id \ --additional-attr=gene_name \

Answer 1

[Istvan Albert]

look at your annotation file, that is where the discrepancy might be located

[TM]

Thank for your helpful answer, I checked again and found that I used different versions between the index and annotation file.