User: shuelga

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shuelga20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
4 years, 7 months ago
Joined:
5 years, 4 months ago
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s******@gmail.com

Posts by shuelga

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Is there software that takes advantage of MarkedDuplicates for SNP calling?
... Duplicate reads will have the same start coordinate, but may contain different mismatches in the alignment mostly due to sequencing errors, so they may not have the same sequence.  ...
written 4.7 years ago by shuelga20
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Is there software that takes advantage of MarkedDuplicates for SNP calling?
... My usual pipeline for SNP calling is to MarkDuplicate and run GATK HaplotypeCaller. I have read somewhere on the GATK forum that HaplotypeCaller ignores reads that are marked as duplicates, however I think there is something to be learned from the duplicate reads. Ultimately they are a re-sequencing ...
gatk markduplicates snp consensus sequence written 4.7 years ago by shuelga20
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Comment: C: prevent [samopen] from being printed by samtools
... oh! thanks for the tip. i will also update. ...
written 4.8 years ago by shuelga20
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Comment: C: prevent [samopen] from being printed by samtools
... Thanks for a quick response. I tried that and it didn't seem to work, although my call piped output to another call, so I just had to relocate the stderr redirect to the first call and now it works (duh). Thank you! ...
written 4.8 years ago by shuelga20
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prevent [samopen] from being printed by samtools
... I am calling samtools as a subprocess from a script, many times. Each time it runs I get a message to the screen that says "[samopen] SAM header is present: X sequences". I have tried to redirect it, but have not been successful. I don't see any kind of "quiet" mode option in samtools. Is there a wa ...
alignment subprocess samtools written 4.8 years ago by shuelga20 • updated 4.8 years ago by Devon Ryan93k
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Splice-aware insert size for RNA-seq
... Usually for DNA we map PE data to the genome and then use picard's CollectInsertSizeMetrics to give a insert size distribution. For RNA PE data we map to the genome with STAR and then want to look at insert size. I don't think that CollectInsertSizeMetrics will work, since it will think that spliced ...
genome alignment rna-seq written 5.0 years ago by shuelga20 • updated 8 months ago by Biostar ♦♦ 20
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eprimer3 and primer3 incompatible still?
... I am using the most up to date version of emboss (6.6.0) and primer3 (2.3.6), yet I STILL cannot get them to run correctly. I've searched around for a lot of help on this and have followed many of the recommendations, but nothing works. Currently when I run eprimer32 I get a seg fault which I think ...
eprimer3 written 5.4 years ago by shuelga20 • updated 4.7 years ago by Owen S.350

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