Forum: Bioinformatics
01-22-2015, 01:53 PM
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Replies: 7
Views: 1,573
A quick starting point
Here's a starting point for you. I copied the 23mer you provided 3 times with a slight modification to the first occurrence.
=== script.pl ======
#!/usr/bin/env perl
use Data::Dumper;
my...
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Forum: Bioinformatics
06-11-2014, 04:39 AM
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Replies: 3
Views: 3,390
Thanks for the info. No clue why I didn't see...
Thanks for the info. No clue why I didn't see that in the first place. After confirming the left most and right most reads, the orientation of F2R1 as properly paired clicked in. Thanks again!
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Forum: Bioinformatics
06-10-2014, 04:50 AM
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Replies: 3
Views: 3,390
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Forum: Bioinformatics
06-27-2013, 05:51 PM
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Replies: 8
Views: 1,961
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Forum: Bioinformatics
06-26-2013, 04:27 AM
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Replies: 8
Views: 1,961
Data Pipeline Automation, what are you using?
I'm curious to know what type of pipeline workflow automation tool people are using these days. At the start of my career, I started cobbling together various shell scripts which quickly turned into...
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Forum: Bioinformatics
01-25-2013, 04:52 AM
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Replies: 3
Views: 1,345
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Forum: Bioinformatics
01-22-2013, 11:50 AM
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Replies: 3
Views: 1,345
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Forum: Bioinformatics
01-05-2013, 03:34 PM
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Replies: 8
Views: 5,190
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Forum: Bioinformatics
01-05-2013, 09:46 AM
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Replies: 8
Views: 5,190
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Forum: Bioinformatics
01-05-2013, 03:44 AM
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Replies: 8
Views: 5,190
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Forum: General
02-01-2012, 07:42 AM
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Replies: 4
Views: 1,725
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Forum: Bioinformatics
10-18-2011, 09:23 AM
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Replies: 9
Views: 15,365
With BWA output, I usually use Picard's...
With BWA output, I usually use Picard's AddOrRemoveReadGroups.jar before feeding the BAM file to GATK. You can provide all the necessary read group details to ensure GATK works.
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Forum: Bioinformatics
07-31-2011, 07:21 PM
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Replies: 2
Views: 1,470
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Forum: Bioinformatics
06-10-2011, 06:12 PM
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Replies: 27
Views: 10,837
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Forum: Bioinformatics
05-07-2011, 04:25 PM
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Replies: 1
Views: 3,550
Looks like it was a simple solution. Needed to...
Looks like it was a simple solution. Needed to upgrade to the latest version of Samtools (we were using 0.1.12) . Seems like that version of Samtools will use only properly paired reads in the BAM...
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Forum: Bioinformatics
05-06-2011, 12:15 PM
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Replies: 1
Views: 3,550
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Forum: Bioinformatics
02-27-2011, 03:09 PM
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Replies: 1
Views: 1,614
SHRiMP2 for smRNA
I've been working with smRNA data for the last little while trying to come up with a pipeline to replace the AB smRNA tools that we were previously using for SOLiD data. I'm curious to know what...
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Forum: Bioinformatics
01-24-2011, 03:28 AM
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Replies: 6
Views: 2,815
BFAST submission to SGE script
Has anyone tried the bfast.submit.pl tool to submit jobs to an SGE cluster? If yes, can you provide an example config script?
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Forum: Bioinformatics
01-21-2011, 09:28 AM
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Replies: 0
Views: 2,257
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Forum: Bioinformatics
01-04-2011, 08:49 AM
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Replies: 6
Views: 1,889
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Forum: SOLiD
12-11-2010, 08:00 PM
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Replies: 5
Views: 5,838
miRNA * non* forms and hairpin
I've been working with the SOLiD smRNA pipeline and have been questioning the genome alignment portion.
I've been using Bioscope to directly align the smRNA reads to the whole genome as 1x36...
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Forum: Bioinformatics
12-09-2010, 02:26 PM
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Replies: 1
Views: 1,085
IRC channels
Does anyone know of any good IRC channels to discuss bioinformatics? I noticed #bioperl and received a tweet about #bioruby from @mza.
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Forum: Bioinformatics
12-09-2010, 02:28 AM
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Replies: 5
Views: 2,282
Thanks for the tip Kevin. I ended up making a...
Thanks for the tip Kevin. I ended up making a change to our grid engine (implemented consumables for memory and expanded a queue the number of nodes being used) and all is fine. I'm quite impressed...
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Forum: Bioinformatics
11-29-2010, 06:38 PM
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Replies: 5
Views: 2,282
Thanks for the advice. I've implemented the...
Thanks for the advice. I've implemented the change as per your recommendation. Unfortunately it didn't resolve my issue. I'm digging into the logs and can hopefully provide an update here to help...
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Forum: Bioinformatics
11-28-2010, 05:46 PM
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Replies: 5
Views: 2,282
Bioscope 1.3 Error, suggestions anyone?
I've installed and am currently running the latest version of Bioscope (v1.3) on some test data set. All the demos that accompanied Bioscope 1.3 worked flawlessly but running one of our standard...
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