Forum: Events / Conferences
02-10-2014, 07:23 AM
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Replies: 4
Views: 1,729
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Forum: Events / Conferences
02-07-2014, 01:46 PM
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Replies: 4
Views: 1,729
Agbt2014
Anyone planning a get together at AGBT? I'm sure we could find some free drinks! :D
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Forum: Ion Torrent
12-13-2013, 05:46 AM
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Replies: 5
Views: 3,782
Not sure. All I know is that there are several...
Not sure. All I know is that there are several 9-15bp indels that are Sanger validated that are not getting aligned. I know BWA will not usually align reads with indels > 8bp, but Novoalign does. ...
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Forum: Ion Torrent
12-09-2013, 10:49 AM
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Replies: 5
Views: 3,782
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Forum: RNA Sequencing
12-06-2013, 10:07 AM
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Replies: 3
Views: 2,321
I hadn't actually seen it before, but it is a...
I hadn't actually seen it before, but it is a very good looking web app! The power estimates should be similar, but won't be identical for 2 reasons:
1. Scotty assumes that variance follows a...
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Forum: RNA Sequencing
12-06-2013, 09:16 AM
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Replies: 3
Views: 2,321
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Forum: Ion Torrent
12-06-2013, 07:59 AM
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Replies: 5
Views: 3,782
Primer Sequences for Cancer Panels
Does anyone know what the exact primer sequences are for the cancer panels? I really need to know so I can remove them during the alignment step. Otherwise it causes certain indels to be missed.
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Forum: Genomic Resequencing
08-25-2013, 08:13 PM
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Replies: 2
Views: 1,807
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Forum: Bioinformatics
01-16-2013, 10:02 PM
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Replies: 3
Views: 1,228
Ryan,
I wrote SoftSearch and would be happy to...
Ryan,
I wrote SoftSearch and would be happy to help if you're interested. I'm updating the website regularly with improvements, trying to get ready for paper submission, so make sure you use the...
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Forum: Bioinformatics
11-02-2012, 11:54 AM
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Replies: 0
Views: 913
Visualizing Integrated data
All,
Several papers are coming out now with plots that show the type and frequency of somatic mutaions, CNV, expression, etc. One example is from this paper here...
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Forum: Genomic Resequencing
08-14-2012, 08:25 PM
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Replies: 2
Views: 1,710
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Forum: Bioinformatics
07-11-2012, 03:07 PM
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Replies: 6
Views: 4,473
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Forum: Bioinformatics
07-11-2012, 09:03 AM
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Replies: 6
Views: 4,473
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Forum: Bioinformatics
06-06-2012, 04:35 AM
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Replies: 10
Views: 3,256
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Forum: Bioinformatics
04-10-2012, 05:56 AM
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Replies: 12
Views: 4,667
@RockChalkJayhawk and others who have used...
@RockChalkJayhawk and others who have used BreakDancer
I'm running some 100GB whole genome Illumina sequencing files on BreakDancer. The program has been running for 2 weeks and has done 500...
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Forum: Bioinformatics
03-27-2012, 02:00 PM
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Replies: 10
Views: 2,350
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Forum: Bioinformatics
03-27-2012, 11:57 AM
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Replies: 10
Views: 2,350
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Forum: Bioinformatics
03-27-2012, 07:48 AM
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Replies: 10
Views: 2,350
pileup2bam
Anyone aware of a tool that can convert a pileup file to BAM files.
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Forum: Bioinformatics
03-21-2012, 05:45 AM
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Replies: 10
Views: 3,256
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Forum: Bioinformatics
03-10-2012, 07:20 AM
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Replies: 12
Views: 4,667
I usually take a 3-tiered approach, using...
I usually take a 3-tiered approach, using CNVnator (read Depth), Break Dancer (Read pair) and CREST (split read). However, I too see a lot fo false positives from each tool. What would be great is...
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Forum: Bioinformatics
03-10-2012, 07:13 AM
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Replies: 2
Views: 5,048
SomaticSniper filtering
I too have had this problem with SomaticSniper. I reccomend filtering out those call where 5% of the alternate allele can be found in the normal sample. I would be interested in Someone from Wash U...
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Forum: Bioinformatics
02-25-2012, 03:52 PM
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Replies: 3
Views: 1,397
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Forum: Bioinformatics
02-24-2012, 11:47 AM
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Replies: 1
Views: 2,038
from the README
The program will...
from the README
The program will generate a *.predSV.txt file. The filename will be the input
bam with .predSV.txt appended unless you specify the -p parameter. Also the
STDERR output has...
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Forum: Bioinformatics
02-09-2012, 08:37 AM
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Replies: 9
Views: 5,429
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Forum: Bioinformatics
02-09-2012, 06:10 AM
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Replies: 9
Views: 5,429
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