Editing
Kun:LabNotes/MONOD/2014-8-12
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===1. Compile a list of RRBS targets=== *Take all the RRBS data that we generated from primary tumor samples, concatenate all the methylFreq files, and generate a single BED file. cat 6-T-1_1.methylFreq 6-T-1_2.methylFreq 6-T-2_1.methylFreq 6-T-2_2.methylFreq 6-T-3_1.methylFreq 6-T-3_2.methylFreq 6-T-4_1.methylFreq 6-T-4_2.methylFreq 6-T-5_1.methylFreq 6-T-5_2.methylFreq 7-T-1_1.methylFreq 7-T-1_2.methylFreq 7-T-2_1.methylFreq 7-T-2_2.methylFreq 7-T-3_1.methylFreq 7-T-3_2.methylFreq 7-T-4_1.methylFreq 7-T-4_2.methylFreq 7-T-5_1.methylFreq 7-T-5_2.methylFreq CTT-FFPE-100ng_1.methylFreq CTT-FFPE-100ng_2.methylFreq CTT-FFPE-5ng_1.methylFreq CTT-FFPE-5ng_2.methylFreq CTT-frozen-100ng_1.methylFreq CTT-frozen-100ng_2.methylFreq CTT-frozen-5ng_1.methylFreq CTT-frozen-5ng_2.methylFreq PC-T-1_1.methylFreq PC-T-1_2.methylFreq PC-T-2_1.methylFreq PC-T-2_2.methylFreq PC-T-4_1.methylFreq PC-T-4_2.methylFreq PC-T-6_1.methylFreq PC-T-6_2.methylFreq PC-T-7_1.methylFreq PC-T-7_2.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 20 > /home/kunzhang/CpgMIP/Data/MONOD/MONOD_primary_tumor_RRBS_combined.BED.txt cat MONOD_primary_tumor_RRBS_combined.BED.txt | sort -k1,1 -k2,2n > MONOD_primary_tumor_RRBS_combined.sorted.BED.txt *Group the sites covered into clusters: ./[[Media:bed2Clusters.txt|bed2Clusters.pl]] MONOD_primary_tumor_RRBS_combined.sorted.BED.txt > [[Media:MONOD_primary_tumor_RRBS_targets.BED.txt|MONOD_primary_tumor_RRBS_targets.BED.txt]] *A total of 198,439 regions in the autosomes, with a total size of 48.8Mb. *I also compiled a more stringent list of target by requiring a minimal read depth of 100 for the CpG sites. This list has 119,966 autosomal regions, with a total size of 25.8Mb. awk ' $5>100 { print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9 }' MONOD_primary_tumor_RRBS_combined.sorted.BED.txt > MONOD_primary_tumor_RRBS_combined_RD100.sorted.BED.txt ./bed2Clusters.pl MONOD_primary_tumor_RRBS_combined_RD100.sorted.BED.txt > [[Media:MONOD_primary_tumor_RRBS_targets_RD100.BED.txt|MONOD_primary_tumor_RRBS_targets_RD100.BED.txt]]
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information