Stephen Johnson
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Thank you for this example of how to use AddOrReplaceReadGroups! Would a specified RGPU also be a required for this to run?
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Yes, I was able to fix the read group errors I was getting. Sorry for not replying with the solutio earlier. The solution was to specify the read group information with RGID, RGLB, RGPL, RGSM tags ...
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Thanks for your response. To clarify my last post, I do still get MATE_NOT_FOUND errors when I add read group information with AddOrReplaceGroups, and FixMateInformation does not solve the issue. T...
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Okay, I added the ID tag to the AddOrReplaceGroups command but still got the same "Error:: MATE_NOT_FOUND errors. I also figured out how to add the read groups during alignment and tried that but s...
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Hi, I think it should alternatively be possible to add the read group information during the mapping step, but I've read some posts on that and am having trouble understanding how. I've read that i...
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Hi Genevieve Brandt (she/her), Thanks for your reply. I already get the following error on my sam file immediately downstream of reference genome alignment: ERROR::MISSING_READ_GROUP:Read groups is...
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I tried aligning the one of the affected Libraries (sequenced over two lanes) again with bwa-mem to generate two sam files, but this time used the -M tag to make sure secondary hits are tagged appr...