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Forum: Bioinformatics 03-06-2013, 10:32 AM
Replies: 0
Views: 2,021
Posted By User001
HugeSeq Pipeline

Does anyone have experience using the HugeSeq pipeline (link below)?
http://hugeseq.snyderlab.org/?d1319850

The tools in the pipeline are pretty mainstream (eg BWA, SAMtools, GATK,...
Forum: Illumina/Solexa 03-01-2013, 10:51 AM
Replies: 3
Views: 3,370
Posted By User001
Your logic sounds good. We are also using...

Your logic sounds good. We are also using Nextera but have not tried to change the tagmentation reaction time.
Forum: Epigenetics 02-28-2013, 08:37 AM
Replies: 5
Views: 7,790
Posted By User001
Has anyone tried using MethylMiner to enrich DNA...

Has anyone tried using MethylMiner to enrich DNA that has been tagged and fragmented by Nextera? I would like to try this protocol, but it would be nice to hear others input before potentially...
Forum: Genomic Resequencing 02-15-2013, 08:45 AM
Replies: 1
Views: 20,061
Posted By User001
In case anyone is curious, we decided to keep...

In case anyone is curious, we decided to keep families on the same 96 well prep-plate and randomize 48 cases and 48 controls to each plate. This should minimize enrichment-effects among families and...
Forum: Illumina/Solexa 02-15-2013, 08:31 AM
Replies: 6
Views: 3,299
Posted By User001
We're working on installing CASAVA on a cluster...

We're working on installing CASAVA on a cluster using a Torque/Maui scheduler. Does anyone have a good guide for this? hpcguy do you have some advice?
Forum: Genomic Resequencing 10-18-2012, 02:12 PM
Replies: 1
Views: 20,061
Posted By User001
How to randomize for sample multiplexing and flow cell placement?

We’re about to start targeted sequencing for a study with about 1500 samples (500 trios). The samples will be multiplexed at 96x per flow cell lane.

Does anyone have suggestions on how to...
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