Forum: General
04-30-2012, 01:14 AM
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Replies: 2
Views: 4,155
Hi,
The project fell by the wayside in the...
Hi,
The project fell by the wayside in the end unfortunately.
I heard numerous claims that DSN normalization works very well but only in the right hands - it seems to be a temperamental...
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Forum: Bioinformatics
04-24-2012, 08:37 AM
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Replies: 0
Views: 1,778
What is your approach to variant filtering?
While looking at some exome data I was struck by how widely my final variant list varies using different approaches. Using variant score reclalibration alone with GATK I ended up with 40,000...
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Forum: General
02-29-2012, 02:55 PM
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Replies: 56
Views: 94,253
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Forum: General
02-29-2012, 11:34 AM
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Replies: 56
Views: 94,253
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Forum: Bioinformatics
01-09-2012, 12:52 AM
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Replies: 14
Views: 4,129
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Forum: Bioinformatics
01-06-2012, 01:30 AM
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Replies: 14
Views: 4,129
Nils,
I interleaved the two files and have...
Nils,
I interleaved the two files and have run them using Bfast. However, whenever I reach the postprocess stage, I am not getting successful pairing of the reads regardless of what I specify on...
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Forum: Bioinformatics
01-05-2012, 05:15 AM
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Replies: 14
Views: 4,129
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Forum: Bioinformatics
01-04-2012, 03:58 AM
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Replies: 14
Views: 4,129
Using Bfast to align paired end Illumina reads
Hi,
I am attempting to align paired end Illumina reads to the human genome with Bfast.
The problem is that most aligners expect paired end reads in 2 fastq files while Bfast expects 1 file. ...
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Forum: Bioinformatics
12-08-2011, 01:03 AM
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Replies: 1
Views: 1,618
Bfast, single end reads and large indels
Hi,
I am wondering what the largest indels I can theoretically detect with Bfast and single end 90bp reads are? Has anyone got experience in this? Come on Nils - I know you must have :D
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Forum: Bioinformatics
12-06-2011, 12:52 AM
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Replies: 7
Views: 4,478
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Forum: Bioinformatics
12-05-2011, 08:23 AM
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Replies: 7
Views: 4,478
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Forum: Bioinformatics
12-05-2011, 06:40 AM
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Replies: 7
Views: 4,478
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Forum: Bioinformatics
12-05-2011, 03:48 AM
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Replies: 7
Views: 4,478
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Forum: Bioinformatics
12-05-2011, 01:23 AM
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Replies: 7
Views: 4,478
6-99bp indels with BWA/GATK
Hi,
I am using BWA and GATK to detect mutations in BRCA1. The BRCA1 sequences have been Sanger validated and contain known mutations. I am achieving a fair degree of accuracy so far,...
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Forum: Bioinformatics
11-30-2011, 03:16 AM
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Replies: 3
Views: 2,836
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Forum: Bioinformatics
11-29-2011, 08:15 AM
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Replies: 3
Views: 2,836
Comparing and combining vcf files
Hi,
I am trying to determine if there is an available solution for comparing vcf files and combining them into a single, non-redundant file?
So for example, if I have two vcf files for two...
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Forum: Ion Torrent
11-22-2011, 04:46 AM
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Replies: 1
Views: 2,332
Sequence biases toward read ends
I'm just having a look at the publicly available DH10B data with the FastQC program and notice some pretty huge spikes in sequence bias at the 3' end, with smaller rises at the 5` end. Being new to...
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Forum: General
11-10-2011, 07:57 AM
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Replies: 3
Views: 3,717
Nick, can I just follow this up?
Between...
Nick, can I just follow this up?
Between MiSeq and Ion Torrent - which do you see having the greater clinical application (generally)?
Also, more specifically are the homopolymers likely to be...
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Forum: General
11-09-2011, 12:52 AM
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Replies: 3
Views: 3,717
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Forum: General
11-08-2011, 02:45 AM
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Replies: 3
Views: 3,717
SNP/Indel analysis and homopolymer errors
Hi,
I am wondering what the general consensus is on SNP/Indel detection from resequencing data generated by homopolymer error-prone platforms like 454 and Ion torrent?
Off the top of my head I...
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Forum: Bioinformatics
09-21-2011, 08:23 AM
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Replies: 4
Views: 3,954
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Forum: Bioinformatics
09-15-2011, 02:59 AM
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Replies: 0
Views: 1,312
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Forum: Polonator
08-15-2011, 12:45 AM
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Replies: 11
Views: 72,391
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Forum: General
08-13-2011, 05:14 AM
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Replies: 6
Views: 2,852
Approximately 50 samples for the purpose of...
Approximately 50 samples for the purpose of SNP/Indel analysis and genotyping. I had assumed 454 technology would be no good here because of the Indels. So it's OK to use traditional PCR approaches...
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Forum: De novo discovery
08-12-2011, 05:22 AM
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Replies: 3
Views: 2,437
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