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derele / AA_Metabarcoding

Analysing multi-marker metabarcoding
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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)

derele commented 5 years ago

Hi Arman,

what a great project! I know the problem and have misused the parameter for 10years. I'll change it, thanks for the reminder!

Cheers Emanuel

On Sun, 30 Sep 2018, 08:30 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/derele/AA_Metabarcoding/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AAI5NG7N-oUao5_ljTh0I8gxmBSDpZdiks5uf_SQgaJpZM4XAtlw .