Question: what is tAKR in the last of htseq results.
0
gravatar for chunxuan
5.2 years ago by
chunxuan10
Germany
chunxuan10 wrote:

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?

 

rna-seq • 1.7k views
ADD COMMENTlink written 5.2 years ago by chunxuan10

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

ADD REPLYlink written 5.2 years ago by Devon Ryan91k
4
gravatar for Martombo
5.2 years ago by
Martombo2.5k
Seville, ES
Martombo2.5k wrote:

I'd guess it is a gene: https://www.google.ch/search?q=takr+gene&oq=takr+gene&aqs=chrome..69i57j0l5.2543j0j7&sourceid=chrome&es_sm=125&ie=UTF-8#nfpr=1&q=takr+gene

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

ADD COMMENTlink written 5.2 years ago by Martombo2.5k

@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?

ADD REPLYlink written 5.2 years ago by chunxuan10

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

@Martombo: Good catch!

ADD REPLYlink written 5.2 years ago by Devon Ryan91k
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