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HT-Seq, Gene ID appeared in Gene Name row

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!enter image description here

rna-seq output counting table ht-seq
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updated by Istvan Albert Istvan Albert • written by TM • TM

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

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written by abedkurdi10 • abedkurdi10

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?

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written by TM • TM

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

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written by Istvan Albert Istvan Albert

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 \

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written by TM • TM

1 answer

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

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written by Istvan Albert Istvan Albert

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

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written by TM • TM

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