Stephen Johnson
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Activity overview
Latest activity by Stephen Johnson-
Stephen Johnson commented,
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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Stephen Johnson commented,
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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Stephen Johnson commented,
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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Stephen Johnson commented,
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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Stephen Johnson commented,
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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Stephen Johnson created a post,
ValiidateSamFile Error: Mate not found
AnsweredHello, I'm a relatively new user trying to generate bam files for SNP calling. I'm using the latest version of Picard (2.25.6). My basic pipeline is to: 1) trim low quality sequences and adapters w...
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Stephen Johnson created a post,
Updating Picard to latest version
AnsweredBefore asking for help with specific errors I'd like to update the version of Picard I'm using to the most recent. Is this possible to do without completely deleting and reinstalling the Program?
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Stephen Johnson commented,
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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Stephen Johnson commented,
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...
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Stephen Johnson created a post,
Error: ValidateSamFile Value was put into PairInfoMap more than once.
I tried running ValidateSamFile on a bam file (to troubleshoot a different problem), but got an error message stating that "ValidateSamFile Value was put into PairInfoMap more than once" This bam f...