Kun:LabNotes/MONOD/2014-11-22: Difference between revisions
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==Nimblegen capture of blood LMS regions== | ==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. | *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: [[Media:UCSD_Zhang_UMR_27Aug2014.bed.txt|UCSD_Zhang_UMR_27Aug2014.bed]]. Nimblegen returned a list of targets covered by their probes. [[Media:OID42096_hg19_UMR_v1_capture_targets.bed.txt|OID42096_hg19_UMR_v1_capture_targets.bed]]. | ||
*Library preparation & capture: [[Noi/NOTES/2014-10-29]], [[Noi/NOTES/2014-11-4]] | *Library preparation & capture: [[Noi/NOTES/2014-10-29]], [[Noi/NOTES/2014-11-4]] | ||
*Read mapping: [[Dinh/Dinh_2014/NOTES/2014-11-17]] | *Read mapping: [[Dinh/Dinh_2014/NOTES/2014-11-17]] |
Revision as of 06:03, 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