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Forum: Sample Prep / Library Generation 10-05-2012, 04:04 AM
Replies: 0
Views: 1,665
Posted By ugm6hr
PCR-based target resequencing with Illumina

I have enriched exonic regions of candidate genes with Fluidigm Access Array (microfluidic PCR-based) to create libraries from human DNA. The resequencing is on Illumina HiSeq.

Does anyone have...
Forum: Sample Prep / Library Generation 10-05-2012, 03:57 AM
Replies: 2
Views: 3,070
Posted By ugm6hr
This makes perfect sense, but I didn't want to...

This makes perfect sense, but I didn't want to deviate from their published protocols for my experiment.
If you do use an alternate dilution / number of PCR cycles, I'd be interested to hear the...
Forum: Bioinformatics 10-05-2012, 03:52 AM
Replies: 2
Views: 1,583
Posted By ugm6hr
Thanks adaptivegenome. That is beyond my...

Thanks adaptivegenome.
That is beyond my programming skills. I was hoping that someone may have done something similar already...
I may make do with the BamUtil: stats Q20% as an alternative way of...
Forum: Bioinformatics 10-04-2012, 01:48 AM
Replies: 2
Views: 1,583
Posted By ugm6hr
Extract mean mapped base phred quality by mapped location from BAM file

I would like to display a histogram of mean mapped base phred quality (call quality, not mapping quality), with chromosomal location on the "x-axis"
I have recalibrated & realigned BAM files from...
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