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Confirm that use of BLAST's `-max_target_seqs` is intentional #1

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)

evansbenj commented 5 years ago

Hi Arman,

Thank you very much for contacting us. You are correct - we misinterpreted the meaning of this flag and this probably affects our pipeline. I appreciate the scientific citizenship it took to contact us!

Ben

Ben Evans Biology Department McMaster University Life Sciences Building room 328 1280 Main Street West Hamilton, Ontario L8S4K1 Canada phone (office/lab) : 905-525-9140 x 26973/27261 fax: 905-522-6066 Lab Website: http://benevanslab.wordpress.com/ http://benevanslab.wordpress.com/

On Sep 29, 2018, at 6:34 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:

Documentation/evolution_of_sex_biased_genes/orthologs_identification_unigene_approach.md https://github.com/evansbenj/Ideas_for_Xue/blob/1bf577de8e013351e81f639f247c1a38ea5fb1e6/Documentation/evolution_of_sex_biased_genes/orthologs_identification_unigene_approach.md 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/evansbenj/Ideas_for_Xue/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AL1sOd24xuFMxGQzQ21sfNYXer1OygMEks5uf_VrgaJpZM4XAtql.