Best way to attach go terms to blast output

[ocattau]

So I have my blast output from the larval geoduck transcriptome here and I the end goal is to characterize Functional Annotations of the genes see issue post. The format is in

• target _id
• uniprot identifiers (accession_Id)
• counts (length, eff_length, est_counts, tpm...)

Eventually I want go terms, protein names etc... in order to say something meaningful about geoduck larval development. Is there a tutorial already that shows how to do this?

[kubu4]

Unfortunately, I don't think any tutorial/example has been fully fleshed out. There are a few things that have been started, but are incomplete. With that being said, here's my recommendations.

For the most reproducible process, I'd recommend looking at this notebook entry (https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20210601_ssal_gff-annotations.ipynb), starting at In[12]. Basically, here's the process that needs to take place:

1. Get a newline-delimited file of SP IDs from your BLAST output.
2. Modify the Perl script that's show in In[13] to work with SPIDs (replace P_ENTREZGENEID with SWISSPROT)
3. Run the updated Perl script.
4. Parse out all of the stuff you want (example is shown in In[18]).
5. Join this with your BLAST output. There's an example of this in In[22], but you'll need to modify it to work with your BLAST output file.

That will get you a lot of the info you want.

After that, you'll likely want to get GOslims. The next step towards that would be to "unfold" the file you created in Step 5 above. There's a script that will do this for you here:

• https://github.com/RobertsLab/code/blob/master/script-box/gigas_go_unfold.sh

Once you get through this stuff, we'll tackle getting GOslims!

EDITED: Add forgotten notebook link!

[sr320]

It is also ok to "just join" with Swiss-prot annotation table - available via https://d.pr/i/0ZO1bc

see also https://github.com/RobertsLab/code/blob/master/10-blast-2-slim.ipynb

[ocattau]

oh okay, thats what I did before but now I see the Go terms. Thanks!