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RichieJu520 / Metagenomics-workshop-on-euler

A workshop for microbial metagenomics and bioinformatics practice on the euler server of ETH Zurich
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Confirm that use of BLAST's `-max_target_seqs` is intentional #1

Open armish opened 6 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)

RichieJu520 commented 6 years ago

Dear Arman,

Thank you for your responsible notification on this issue. I used the lsf script for workshop demonstration purpose, but I am sure that many researchers set -max_target_seq as one to retrieve best hits (i.e., hits with the maximum bit score). I noticed this paper earlier and will pay attention to how the BLAST authors will respond to this issue.

Cheers, Feng

B. Arman Aksoy notifications@github.com 于2018年9月30日周日 上午12:18写道：

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 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/RichieJu520/Metagenomics-workshop-on-euler/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AM4Ton7uQldU9YGocRduqYD1rhuzdttTks5uf_GjgaJpZM4XAtVc .

-- Feng JU, Ph. D. Postdoctoral Scientist Microbial Ecology Group, Department of Surface Waters Swiss Federal Institute of Aquatic Science and Technology (eawag) Seestrasse 79, 6047 Kastanienbaum Switzerland Phone: +41 58 765 2163 Fax: +41 58 765 2168 http://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/feng-ju/