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Adjust the name of monomer/walk tag in digest to compatibility with pairtools #10

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LuJiansen opened this issue Jul 30, 2024 · 2 comments
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Adjust the name of monomer/walk tag in digest to compatibility with pairtools #10

LuJiansen opened this issue Jul 30, 2024 · 2 comments

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@LuJiansen
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LuJiansen commented Jul 30, 2024 •
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Hi, I'm trying to convert the pore-c-py digested bam into .pairs format and extract the SAM tags including monomer tag Xc and walk tag Xw as extra column in the .pairs file. However, the pairtools only supports SAM tag with pair of uppercase letters. Could you please adjust the name of these tags of give a option for users to define them? Thanks!
@cjw85
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cjw85 commented Jul 30, 2024

The lowecase letters indicate that these tags are not formally defined by the Sam tags specification. They are deliberately not uppercase. See https://samtools.github.io/hts-specs/SAMtags.pdf

In that sense this is a bug in pairtools not pore-c-py.

@LuJiansen
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Thank you for your prompt reply!

@LuJiansen LuJiansen mentioned this issue Jul 30, 2024
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@cjw85 @LuJiansen