Question: How to annotate Diamond output files
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gravatar for biohacker_tobe
11 weeks ago by
biohacker_tobe40 wrote:

I have done the aligning of my protein sequences and of short reads against a protein reference database using diamond. However I would like to annotate my alignments but I would prefer to do this on bash. I found this https://resources.qiagenbioinformatics.com/manuals/clcmgm/current/index.php?manual=Annotate_with_DIAMOND.html to be useful but this is a seperate software.

Question: Is it is possible to annotate this alignment created from Diamond within bash?

alignment • 150 views
ADD COMMENTlink written 11 weeks ago by biohacker_tobe40

Hi,

First of all, what do you mean with "annotate". If you are simply talking about adding names/descriptions to your alignments, you can easily do it with grep, awk, sed, etc, depending on what format of your outputs (e.g. if you got any tabular file of your input/query IDs versus your hits/subject IDs). Also, the proteins database is a well documented/curated one (like nr, refseq, swissprot) or is it a cusomized set of yours?

Cheers

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Arsenal20
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