Kun:LabNotes/MONOD/2013-11-22: Difference between revisions
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===Probe design=== | ===Probe design=== | ||
*I designed two sets of probes, one with ~150bp gap size and the other with ~400bp gap size. | |||
**Target file: [[Media:targetFile_MONOD_v1.txt|targetFile_MONOD_v1.txt]] | |||
**ppDesigner output | |||
***150bp probes: [[Media:ppDesigner_out_150bp_MONOD_v1.txt|ppDesigner_out_150bp_MONOD_v1.txt]] | |||
***400bp probes: [[Media:ppDesigner_out_150bp_MONOD_v1.txt|ppDesigner_out_150bp_MONOD_v1.txt]] | |||
===BSPP capture=== | ===BSPP capture=== | ||
===Data analysis=== | ===Data analysis=== |
Revision as of 03:28, 19 March 2014
MONOD round 1
Target identification
- Data used:
- Cancer data:
- GBM: U87 (ENCODE RRBS Hudson Alpha; ENCODE 450k)
- Pancreatic cancer: PANC1 (ENCODE RRBS UW & Hudson Alpha; ENCODE 450k)
- Whole blood data: GSE30253 RRBS data; GSE31263 WGBS data
- Cancer data:
- DMSs and DMS clusters identification:
- I wrote a simple script that takes the average of all existing data for each CpG site, and reported the sites at which the methylation difference was greater than 0.8 between cancer and whole blood.
./find_DMS_MONOD_v1.pl > MONOD_v1_DMS.txt
- These sites were then grouped into DMS clusters.
./extract_clusters.pl MONOD_v1_DMS.txt > MONOD_v1_DMS_clusters.txt
Probe design
- I designed two sets of probes, one with ~150bp gap size and the other with ~400bp gap size.
- Target file: targetFile_MONOD_v1.txt
- ppDesigner output
- 150bp probes: ppDesigner_out_150bp_MONOD_v1.txt
- 400bp probes: ppDesigner_out_150bp_MONOD_v1.txt