Annotations

[Rajashree93]

Hello,

I am trying the annotation module Annotate binding sites to genes and using gencode.v40.sorted.gtf (https://www.gencodegenes.org/human/) as gtf file.

Many of the pairs that are found from the same bed files are returning output as follows - no annotation found even thought the pair is present in the data/bed file. Some are returning annotations.

I need to understand the inventor's opinion on both the cases - what does it mean to have a gene annotation of a particular TF pair? What does it mean when you don't get any return for your annotation?

[msbentsen]

Hi @Rajashree93 ,

Please use the issues page for TF-COMB if your issue relates specifically to this software, thanks. I have automatically transferred the other issues. You can find the page here: https://github.com/loosolab/TF-COMB/issues

[msbentsen]

Hi @Rajashree93

I need to understand the inventor's opinion on both the cases - what does it mean to have a gene annotation of a particular TF pair? What does it mean when you don't get any return for your annotation?

If you find annotation for some pairs but not for others, a missing annotation can be interpreted as this TF pair was not found near any genes in the .gtf file. For example, if TF's are found in distal chromatin regions, they are not annotated to genes but might still be important in other contexts. You might also try to adjust the annotation parameters in order to find more/annotations by using custom_config as described in the documentation here: https://tf-comb.readthedocs.io/en/latest/API/tfcomb.annotation.html#tfcomb.annotation.annotate_regions

Hope this helps explain the functionality.

[vheger]

I will close this for now, since there was no activity for a long time in this Issue.
Please feel free to reopen the Issue if the problem persists.