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Forum: Sample Prep / Library Generation 09-24-2014, 06:42 PM
Replies: 6
Views: 8,384
Posted By yxl
KAPA, dual-SPRI size selection

The KAPA Hyper kit has a protocol for using AMPure beads for size selection (dual-SPRI), but it seems to me that the bead:DNA ratio is off (or perhaps I am not understanding the concept correctly)....
Forum: Bioinformatics 11-14-2012, 02:47 PM
Replies: 2
Views: 2,787
Posted By yxl
How about the ">" or "<" characters in column 5...

How about the ">" or "<" characters in column 5 of the pileup format? I can't seem to find any information about what they signify:

chr1 4483937 G G 48 0 60 7 ...
Forum: Bioinformatics 04-22-2011, 07:07 PM
Replies: 0
Views: 3,263
Posted By yxl
GATK pileup with merged BAM files

I have several lanes of sequences which I have merged into one BAM file. I then processed this merged BAM file through GATK: recal, dedup, etc. I want create a pileup from the merged BAM file using...
Forum: Epigenetics 02-24-2011, 09:09 AM
Replies: 0
Views: 1,588
Posted By yxl
Epigenome reference: BI submissions to SRA

I've been looking at the SRA submissions from the epignome reference mapping project. Looking at:

http://www.genboree.org/epigenomeatlas/edaccDataFreeze2.rhtml

...the BI seems to have run many...
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