Kun:LabNotes/MONOD/2014-11-22: Difference between revisions
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*Read mapping: [[Dinh/Dinh_2014/NOTES/2014-11-17]]. From the fraction of targets covered and the enrichment factors, the data from normal plasma appeared to be much better than the data from cancer patients. | *Read mapping: [[Dinh/Dinh_2014/NOTES/2014-11-17]]. From the fraction of targets covered and the enrichment factors, the data from normal plasma appeared to be much better than the data from cancer patients. | ||
*To take a close look of the read distribution for all these libraries, I extracted the reads for a subset of larger targets (>2k) into smaller bam files for IGV visualization. | *To take a close look of the read distribution for all these libraries, I extracted the reads for a subset of larger targets (>2k) into smaller bam files for IGV visualization. | ||
./[[Media:get_bam_in_targets. | ./[[Media:get_bam_in_targets.txt|get_bam_in_targets.pl]] /media/Ext12T/DD_Ext12T/MONOD/141112_HiSeqRapidRun/BAMfiles | ||
[[Image:plasma_Nimblegen_SeqCap_EPI_bam_plot_1.png|800px]] | [[Image:plasma_Nimblegen_SeqCap_EPI_bam_plot_1.png|800px]] |
Revision as of 06:13, 24 November 2014
Nimblegen capture of blood LMS regions
- Target selection & probe design: I took the UMR regions Dinh called from the PNAS whole blood WGBS data, did "bedtools subtract" to remove the repeats, then select the 32999 regions that were more than 100bp. The total target size is 29.4Mb.
- The target list was submitted to Nimblegen to design customized probes: UCSD_Zhang_UMR_27Aug2014.bed.
- Nimblegen returned a list of targets covered by their probes. OID42096_hg19_UMR_v1_capture_targets.bed.
- Library preparation & capture: Noi/NOTES/2014-10-29, Noi/NOTES/2014-11-4
- Read mapping: Dinh/Dinh_2014/NOTES/2014-11-17. From the fraction of targets covered and the enrichment factors, the data from normal plasma appeared to be much better than the data from cancer patients.
- To take a close look of the read distribution for all these libraries, I extracted the reads for a subset of larger targets (>2k) into smaller bam files for IGV visualization.
./get_bam_in_targets.pl /media/Ext12T/DD_Ext12T/MONOD/141112_HiSeqRapidRun/BAMfiles File:Plasma Nimblegen SeqCap EPI bam plot 1.png