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JiayiQin / MetaAshEnchy

ASHBACK
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Confirm that use of BLAST's `-max_target_seqs` is intentional #2

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)

JiayiQin commented 5 years ago

Hi Arman,

Thanks for your interests in my work. The setting was intentional, as I would like to compare the top 10 output from BLAST results.

Best, Jiayi

armish commented 5 years ago

Hi Jiayi,

As mentioned in that paper, -max_target_seqs X parameter doesn't guarantee that you will get the best X hits but it just guarantees that it will give you X reasonable hits. If I am understanding your code and your comment correctly, you might be misusing this parameter.

Thanks for getting back to me, --Arman