Forum: Bioinformatics
08-03-2011, 06:48 AM
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Replies: 292
Views: 160,451
Dear all,
I'm had the same problem as...
Dear all,
I'm had the same problem as oudacontrol above and Jeckow earlier in this thread.
Trying to get samtools view to extract one chromosome from a sorted and indexed bam file fails:...
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Forum: RNA Sequencing
03-30-2011, 01:41 AM
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Replies: 2
Views: 1,543
"isoforms n.plu. (1) the different forms of a...
"isoforms n.plu. (1) the different forms of a polymorphic protein; (2) two or more proteins or RNAs that are produced from the same gene by differential transcription and/or differential RNA...
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Forum: Bioinformatics
03-30-2011, 01:18 AM
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Replies: 15
Views: 2,841
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Forum: General
03-28-2011, 06:34 AM
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Replies: 11
Views: 3,599
Interesting thread!
Strangely enough (I work...
Interesting thread!
Strangely enough (I work with exomes every day): no, thank you. It's an uncomfortable thought having my sequenced DNA lying around somewhere.
I should in fact take some time...
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Forum: Bioinformatics
03-28-2011, 06:21 AM
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Replies: 1
Views: 4,567
Carefully read your stack trace:
If the...
Carefully read your stack trace:
If the problem isn't the dir you're writing in, use an alternative temp dir (in stead of the default /tmp) with sufficient space (check Picard manual).
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Forum: Bioinformatics
03-23-2011, 02:06 AM
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Replies: 3
Views: 3,293
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Forum: Genomic Resequencing
03-23-2011, 01:40 AM
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Replies: 14
Views: 4,951
Hi,
1. The danger of aligning to only a...
Hi,
1. The danger of aligning to only a certain region is that the aligner will try to find a spot for all reads in that region. This means that reads that do not belong there will be placed...
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Forum: Bioinformatics
03-22-2011, 08:59 AM
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Replies: 7
Views: 3,371
You can also use the GATK.
In case you're...
You can also use the GATK.
In case you're new to the whole thing: I recommend making templates for each of the analysis steps you take, and then run some script to replace the placeholders with...
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Forum: Introductions
03-16-2011, 09:48 AM
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Replies: 4
Views: 3,551
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Forum: Bioinformatics
03-16-2011, 12:56 AM
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Replies: 12
Views: 5,712
Hi John,
Did you already choose and install...
Hi John,
Did you already choose and install a distro, or are you first awaiting some answers here? In that case, the choice for a distro is kind of personal. I'm a Fedora person (have been since...
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Forum: Bioinformatics
03-03-2011, 05:13 AM
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Replies: 11
Views: 4,533
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Forum: Bioinformatics
03-03-2011, 04:46 AM
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Replies: 366
Views: 202,141
Hi Simon and others,
I have a question...
Hi Simon and others,
I have a question regarding thresholds for the per sequence quality scores.
We did a lot of whole exomes on our Illumina machines and for each sample I generate a QC...
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Forum: Bioinformatics
03-03-2011, 03:51 AM
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Replies: 11
Views: 4,533
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Forum: Bioinformatics
03-03-2011, 02:49 AM
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Replies: 11
Views: 4,533
They are.
True.
I haven't used samtools...
They are.
True.
I haven't used samtools tview so I don't know what blue or green means.
I'm not entirely sure I understand your question, so pardon me if I'm telling you stuff you already...
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Forum: Bioinformatics
03-02-2011, 04:56 AM
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Replies: 11
Views: 4,533
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Forum: Bioinformatics
02-23-2011, 12:25 AM
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Replies: 48
Views: 63,436
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Forum: Bioinformatics
02-23-2011, 12:21 AM
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Replies: 1
Views: 3,863
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Forum: Bioinformatics
02-23-2011, 12:00 AM
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Replies: 16
Views: 8,583
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Forum: Bioinformatics
02-22-2011, 08:31 AM
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Replies: 16
Views: 8,583
We see what Westerman said earlier: disk IO...
We see what Westerman said earlier: disk IO trouble. Our solution is access to the university's cluster (http://www.rug.nl/cit/hpcv/publications/docs/millipede), which we share with other research...
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Forum: Bioinformatics
02-10-2011, 01:26 AM
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Replies: 17
Views: 7,753
Were these data sequenced one sample per lane...
Were these data sequenced one sample per lane (which I expect), or multiple samples per lane?
Were other, non cancer cell line samples sequenced on the same run as cancer cell line samples? (I...
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Forum: General
02-10-2011, 12:56 AM
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Replies: 3
Views: 2,038
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Forum: Bioinformatics
02-10-2011, 12:54 AM
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Replies: 48
Views: 63,436
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Forum: Bioinformatics
02-10-2011, 12:50 AM
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Replies: 11
Views: 3,303
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Forum: Bioinformatics
01-27-2011, 01:10 AM
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Replies: 24
Views: 13,627
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Forum: General
01-26-2011, 08:55 AM
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Replies: 18
Views: 7,082
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