Kun:LabNotes/MONOD/2013-11-22: Difference between revisions
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*DMSs and DMS clusters identification: | *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. | **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. | ||
./[[Media:find_DMS_MONOD_v1.txt|find_DMS_MONOD_v1.pl]] > | ./[[Media:find_DMS_MONOD_v1.txt|find_DMS_MONOD_v1.pl]] > MONOD_v1_DMS.txt | ||
**These sites were then grouped into DMS clusters. | **These sites were then grouped into DMS clusters. | ||
./[[Media:extract_clusters.txt|extract_clusters.pl]] | ./[[Media:extract_clusters.txt|extract_clusters.pl]] MONOD_v1_DMS.txt > [[Media:MONOD_v1_DMS_clusters.txt]] | ||
===Probe design=== | ===Probe design=== | ||
===BSPP capture=== | ===BSPP capture=== | ||
===Data analysis=== | ===Data analysis=== |
Revision as of 01:14, 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 > Media:MONOD_v1_DMS_clusters.txt