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enormandeau / go_enrichment

Transcripts annotation and GO enrichment Fisher tests
GNU General Public License v3.0
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Confirm that use of BLAST's `-max_target_seqs` is intentional #3

Closed armish closed 4 years ago

armish commented 6 years ago

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you! -- Arman (armish/blast-patrol)

ViriatoII commented 4 years ago

Hello Eric, Great pipeline, thanks!

I understand that -max_target_seqs 1 does not retrieve the best blast hit, only the first significant one. Do you think this affects very negatively your pipeline? I just got a GO annotation for dendrite development in a plant..

I wonder if it's better to change the blast part to have the best blast hit, or just change the Eval threshold, or even if this problem is irrelevant in the context of annotation.

Cheers, Ricardo

enormandeau commented 4 years ago

Hi, this alert about max_target_seqs generated a lot of discussion when it came out but people were unable to reproduce the problem when they tried, including me. I suggest you try blasting this one sequence on a full database without this option to remove doubt.