Using sample names for proteins in .faa file #205

HilaryESR · 2023-04-11T22:49:29Z

HilaryESR
Apr 11, 2023

Is there a way to make bakta output proteins with the sample name as prefix, instead of what I presume is a locus tag? For example currently outputs are like this:

NPBBKN_00005 UDP-N-acetylglucosamine 1-carboxyvinyltransferase

But I want "NPBBKN" replaced with the name that I specify with the --prefix option.

I need to combine bakta outputs from multiple samples into one file for AMR analysis and currently I have no way of knowing which proteins come from which sample.

oschwengers · 2023-04-12T07:11:46Z

oschwengers
Apr 12, 2023
Maintainer

Via the --prefix option one can set the output file name prefices. I think the best approach to achieve this, is to actually set the locus tag prefix via --locus-tag. By this, you can set distinct locus tags for each sample and thus, proteins can be assigned to their sample.

W/o --compliant: locus tag prefixes must contain between 1 and 24 alphanumeric characters or '_.-' signs.
with --compliant: INSDC Locus tag prefixes must contain between 3 and 12 alphanumeric uppercase characters and start with a letter.

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HilaryESR · 2023-04-12T20:32:29Z

HilaryESR
Apr 12, 2023
Author

Thanks, setting the locus tag works well

0 replies

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Using sample names for proteins in .faa file #205

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Using sample names for proteins in .faa file #205

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HilaryESR Apr 11, 2023

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oschwengers Apr 12, 2023 Maintainer

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HilaryESR Apr 12, 2023 Author

HilaryESR
Apr 11, 2023

oschwengers
Apr 12, 2023
Maintainer

HilaryESR
Apr 12, 2023
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