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ISUgenomics / bioinformatics-workbook

Bioinformatics Workbook repository
https://bioinformaticsworkbook.org
MIT License
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Confirm that use of BLAST's `-max_target_seqs` is intentional #16

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)

aseetharam commented 5 years ago

Thanks for bringing this to our attention. We will keep this issue open until the official Trinotate comes up with suitable solution. We are simply using their recommended steps and will modify when they have the fix.