User: toddknutson

gravatar for toddknutson
toddknutson50
Reputation:
50
Status:
Trusted
Location:
United States
Last seen:
6 months, 1 week ago
Joined:
6 years, 5 months ago
Email:
t**********@gmail.com

about me

Posts by toddknutson

<prev • 14 results • page 1 of 2 • next >
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... @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 toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... No problem! Yes, this is a case where the biology and the informatics are complex and interesting! ...
written 8 months ago by toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 toddknutson50
0
votes
2
answers
658
views
2
answers
Comment: C: How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 toddknutson50
7
votes
2
answers
658
views
6 follow
2
answers
How to retain SEQ and QUAL fields in BAM file after filtering?
... 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 ...
bam samtools bwa written 8 months ago by toddknutson50 • updated 8 months ago by Pierre Lindenbaum122k
0
votes
6
answers
35k
views
6
answers
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 toddknutson50

Latest awards to toddknutson

Supporter 2.1 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 729 users visited in the last hour