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Michigan-Mycology / Lab-Code-and-Hacks

This is the site where we store shared code for the Michigan Mycology Lab
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Confirm that use of BLAST's `-max_target_seqs` is intentional #7

Open armish opened 5 years ago

armish commented 5 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)

wjdavis90 commented 5 years ago

Arman, Thanks for the notification! I will need to review the article, but I am afraid we were unintentionally doing it wrong.

~William

On Sat, Sep 29, 2018 at 6:15 PM B. Arman Aksoy notifications@github.com wrote:

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:

- Genomics/processing_messy_genomic_data/example_megablast_for_esom_script.pbs https://github.com/Michigan-Mycology/Lab-Code-and-Hacks/blob/2b9e4010a7dd5174808280f892d627e4c858d666/Genomics/processing_messy_genomic_data/example_megablast_for_esom_script.pbs

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty833/5106166?redirectedFrom=fulltext, 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 https://github.com/armish/blast-patrol)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Michigan-Mycology/Lab-Code-and-Hacks/issues/7, or mute the thread https://github.com/notifications/unsubscribe-auth/AQY3puDNUTLS8yzx7qYYhizDsWPRjruKks5uf_EHgaJpZM4XAtRi .