User: jason.r.gallant

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Posts by jason.r.gallant

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Comment: C: Mac Osx Confusing Vcf With Vcard
... Great! Thanks for this, My Mac completely runs out of disk space (and thus slows to a halt) because of this problem. ...
written 4.4 years ago by jason.r.gallant10
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Comment: C: Problems With Sam2Pindel
... Hi Kai, Thanks for your note. I am indeed piping samtoolsview into sam2pindel. I wasn't brave enough to just try feeding the bowtie2 bam files directly into pindel :) I will try this now, and see how it goes. I will peek into the bamfile and see if I can send it to you directly. Cheers, Jason ...
written 4.4 years ago by jason.r.gallant10
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Comment: C: Problems With Sam2Pindel
... Nope, no output or log, just hangs. ...
written 4.4 years ago by jason.r.gallant10
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Problems With Sam2Pindel
... Hi all, I'm trying to operate the PINDEL pipeline on some resequencing data that was aligned with Bowtie2. I am starting with the sam2pindel program, and things seem to proceed nicely for several hundred megabytes of output... however the program mysteriously hangs suddenly. Has anyone observed t ...
pindel written 4.4 years ago by jason.r.gallant10 • updated 14 months ago by Biostar ♦♦ 20
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Bioperl Retrieve Fasta Sequence With Colon In Header
... Apologies for cross posting from StackExchange- perhaps this is the more appropriate venue. I'm trying to extract the sequence I need from a database using the following bioperl code: use strict; use Bio::SearchIO; use Bio::DB::Fasta; my ($file, $id, $start, $end) = ("secondround_merged_expande ...
perl fasta bioperl written 4.8 years ago by jason.r.gallant10 • updated 3.5 years ago by Biostar ♦♦ 20

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