what is tAKR in the last of htseq results.

Question

[ccshao]

In the last of HTseq counts result, I found the name of "tAKR", above "no_feature", he "tAKR" is also not mentioned in HTseq document.

The last lines of HTseq result is

tAKR
no_feature
ambiguous
too_low_aQual
not_aligned
alignment_not_unique

It doesn't look like gene names, because the gene names end with "ZZEF1", "ZZZ3". "tAKR" is always 0 (from the data I checked).

Anyone has an idea of what it is?

[Devon Ryan]

Is it in all of the samples or just one? Also, which version of htseq-count are you using?

Answer 1

[Martombo]

I'd guess it is a gene: https://www.google.ch/search?q=takr+gene

why don't you check if it is present in your annotation (GTF file)?

[ccshao]

@Devon Ryan, htseq version is version 0.5.3p9, it is found in all result files.

@Martombo, good suggestion, I should have checked it earlier. Shame. I used the GTF file provieded by Tophat, and it seem like a gene,

gene_id "tAKR"; transcript_id "NR_026743"; gene_name "tAKR"; tss_id "TSS18500";

Do you want to make your comment as a answer?

[Devon Ryan]

I've moved it to an answer for Martombo and it'd be great if you could accept it.

@Martombo: Good catch!