search

LCrossman / Nanopore_urine_analysis

https://www.ncbi.nlm.nih.gov/pubmed/27667325
2 stars 2 forks source link

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

Closed armish closed 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)

LCrossman commented 6 years ago

Dear Arman,

Thanks for your email. I have added a comment to the README on my github that I feel the use of this parameter was justified given the data used at the time which was of low accuracy since it was very early Oxford Nanopore MinION data. On the other hand, anyone looking to use parts of the workflow in future with higher accuracy data should look again at the parameter and quoted the paper in question. best regards, Dr. Lisa Crossman

On Sat, 29 Sep 2018 at 22:42, 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:

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/LCrossman/Nanopore_urine_analysis/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/ALDEl8i1T4H-LzwJjS3VJAfVGh6IyjNgks5uf-lTgaJpZM4XAssH .