Question

trailing paired-end slashes (/) in BAM file

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3 months ago

Matteo Ungaro ▴ 100

Hi there, I'm working with a BAM file to produce a contact-map with PreText. Unfortunately, it appears that trailing /1 and /2 characters after the read name bother the tool which returns an empty map...

Is there a way to get rid of those trailing characters maybe with sed or awk. I've done few experiments, but I guess I'm missing the overall mechanics because it either didn't happen anything, or else the file is corrupted afterwards. Below, it is how the first column of the BAM appears:

E250011414L1C001R00100000217/1
E250011414L1C001R00100000217/1
E250011414L1C001R00100000263/1
.
.
.
E250012634L1C021R01400500123/2
E250012634L1C021R01400500258/2
E250012634L1C021R01400500313/2

Thanks in advance!

awk BAM sed • 344 views

ADD COMMENT • link updated 3 months ago by Ram 44k • written 3 months ago by Matteo Ungaro ▴ 100

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i've done few experiments

show us the commands.

ADD REPLY • link 3 months ago by Pierre Lindenbaum 164k

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Apologies, I haven't been very clear...

ADD REPLY • link 3 months ago by Matteo Ungaro ▴ 100

score 1 · Answer 1 · 2024-07-31

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3 months ago

Pierre Lindenbaum 164k

also: How to remove Read Name (1st column) extension from a BAM file?

ADD COMMENT • link 3 months ago by Pierre Lindenbaum 164k

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@Pierre Lindenbaum that helped, thanks! Tweaking a bit the command gave the expected result!

ADD REPLY • link 3 months ago by Matteo Ungaro ▴ 100