removed max_target_seqs option in blastp process#12
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husensofteng wants to merge 1 commit intolehtiolab:masterfrom
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removed max_target_seqs option in blastp process#12husensofteng wants to merge 1 commit intolehtiolab:masterfrom
husensofteng wants to merge 1 commit intolehtiolab:masterfrom
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Remove the `-max_target_seqs 1` parameter in `blasp` process to avoid early stopping of the algorithm that makes it not find the top best matches. See the references [here](https://gist.github.com/sujaikumar/504b3b7024eaf3a04ef5) and [here](https://doi.org/10.1093/bioinformatics/bty833) https://github.com/lehtiolab/proteogenomics-analysis-workflow/blob/3472dcbaf8b3d20d41a7113519dff691c0a4b0b7/main.nf#L698
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Actually, it turns out there can still be canonical sequences reported as not mapping in blastp. |
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Remove the
-max_target_seqs 1parameter inblaspprocess to avoid early stopping of the algorithm that makes it not find the top best matches.See the references here and here
proteogenomics-analysis-workflow/main.nf
Line 698 in 3472dcb