User: toddknutson
toddknutson • 50
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Posts by toddknutson
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... @Pierre Lindenbaum: I'm glad you posted a link to this answer over on the [Bioinformatics Stack Exchange question][1]. Someone posted a comment there about getting errors downstream when using samtools view, i.e.. [E::sam_parse1] CIGAR and query sequence are of different length. I used `bwa -Y -a` o ...
written 8 months ago by
toddknutson • 50
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... No problem! Yes, this is a case where the biology and the informatics are complex and interesting! ...
written 8 months ago by
toddknutson • 50
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... Awesome! Thanks so much! Our system is currently down for maintenance, but I will fully test ASAP, and then mark as "accepted". ...
written 8 months ago by
toddknutson • 50
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... Thanks for you comment -- you are correct. This is my situation as well. I am working on *PMS2* and *PMS2CL* (pseudogene). My strategy is to map the R1 and R2 reads independently with bwa -a to get all alignments (which results in one alignment being in PMS2 and one being in PMS2CL). This results in ...
written 8 months ago by
toddknutson • 50
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... Thanks, that's a good idea under most circumstances. However, in my situation, I need the supplementary alignments. I am mapping reads against a region that contains both a protein encoding gene and pseudogene, with zero bases that distinguish the two features. Thus, many of my supplementary reads a ...
written 8 months ago by
toddknutson • 50
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... I was thinking about that, but I think there might be some things to consider, regarding reverse and reverse-complement alignments. I saw this [example][1] and gave up trying to write my own script.
[1]: https://www.biostars.org/p/44681/ ...
written 8 months ago by
toddknutson • 50
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... Sure, please let me know if you need anything else! I appreciate your interest/help!
[https://gist.github.com/toddknutson/90430a0dd736898037ed18bcd044df7f][1]
[1]: https://gist.github.com/toddknutson/90430a0dd736898037ed18bcd044df7f ...
written 8 months ago by
toddknutson • 50
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... I'm sorry, but this was not a cross post. I didn't see that other posting after days of google searching! But I appreciate the link to another related question! ...
written 8 months ago by
toddknutson • 50
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... I would like to retain the actual SEQ and QUAL fields in the SAM/BAM file after it has been filtered.
For example, I mapped a single end R1.fastq file. The resulting BAM file contains primary and supplementary alignments (this is especially true when using the `bwa mem -a` flag). Then the BAM was ...
written 8 months ago by
toddknutson • 50
• updated
8 months ago by
Pierre Lindenbaum ♦ 122k
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Comment:
C: Converting Bam To Fastq
... FYI, if you're directly copying this answer, you should use camel case: `SamToFastq` for the program name. Thanks for the answer! ...
written 2.7 years ago by
toddknutson • 50
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