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!
===2. Check the total read depth for CpG sites within the RRBS targets=== cat 6-P-10.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 1 | /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools intersect -wa -a - -b /home/kunzhang/CpgMIP/Data/MONOD/MONOD_primary_tumor_RRBS_targets.BED.txt | /home/kunzhang/CpgMIP/Data/MONOD/bed_total_RD.pl cat 6-P-10.methylFreq | /home/dinh/scripts/methylFreq2BED.pl 1 | /home/kunzhang/CpgMIP/Data/MONOD/bed_total_RD.pl On-target read depth Total CpG read depth % on-target 6-P-10 15,965,319/14,617,979 20,663,932 77.3% 6-P-1 10,145,982/9,347,247 13,357,081 76.0% 6-T-1_1 42,122,819/40,519,748 51,404,477 81.9% 6-T-2_1 39,727,871/38,177,035 47,770,689 83.2% CTT-frozen-100ng_1 50,274,814/48,129,684 55,387,277 90.8% CTT-frozen-5ng_1 14,303,236/13,695,699 15,310,475 93.4% CTT-FFPE-100ng_1 41,695,594/43,527,498 47,409,114 91.8% PC-P-1 6,363,821/5,972,702 7,727,128 82.3% PC-P-10 7,607,573/7,274,238 9,433,521 80.6% PC-T-1_1 44,275,077/42,697,725 53,030,360 83.4% *I believe the on-target rate is an indicator of the degree of DNA fragmentation. If a fraction of DNA are fragmented, they will be included in the sequencing libraries even without MspI digestion. The on-target rate would be lower in such cases. So plasma DNA always have lower on-target rates. *There isn't a big difference between the two sets of target regions identified at different level of stringency. Therefore, I checked the on-target rates for all samples using the larger target set. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Samples''' | align="center" style="background:#f0f0f0;"|'''All sites RD''' | align="center" style="background:#f0f0f0;"|'''On-target RD''' | align="center" style="background:#f0f0f0;"|'''On-target Rate''' |- | 6-P-10||15,965,319||20,663,932||77.3% |- | 6-P-1||10,145,982||13,357,081||76.0% |- | 6-P-2||6,896,186||9,062,234||76.1% |- | 6-P-3||19,268,289||21,802,969||88.4% |- | 6-P-4||5,974,773||7,495,311||79.7% |- | 6-P-5||12,590,365||16,494,290||76.3% |- | 6-P-6||7,512,063||12,272,372||61.2% |- | 6-P-7||11,161,941||15,365,391||72.6% |- | 6-P-8||10,857,495||14,764,214||73.5% |- | 6-P-9||9,301,655||11,828,425||78.6% |- | 6-T-1_1||42,122,819||51,404,477||81.9% |- | 6-T-1_2||55,332,112||68,680,670||80.6% |- | 6-T-2_1||39,727,871||47,770,689||83.2% |- | 6-T-2_2||43,299,367||53,183,818||81.4% |- | 6-T-3_1||36,204,067||45,527,237||79.5% |- | 6-T-3_2||37,657,579||46,334,499||81.3% |- | 6-T-4_1||48,592,836||59,200,663||82.1% |- | 6-T-4_2||44,582,324||52,297,088||85.2% |- | 6-T-5_1||42,943,331||51,084,769||84.1% |- | 6-T-5_2||51,597,080||62,764,249||82.2% |- | 7-P-10||14,120,252||19,830,640||71.2% |- | 7-P-1||18,418,449||22,370,674||82.3% |- | 7-P-2||3,066,869||4,201,304||73.0% |- | 7-P-3||8,092,483||11,658,106||69.4% |- | 7-P-4||16,586,445||20,741,132||80.0% |- | 7-P-5||8,001,688||10,231,049||78.2% |- | 7-P-6||7,444,769||9,792,239||76.0% |- | 7-P-7||10,815,500||13,957,997||77.5% |- | 7-P-8||10,431,532||14,322,889||72.8% |- | 7-P-9||9,590,120||13,362,917||71.8% |- | 7-T-1_1||55,494,618||68,629,065||80.9% |- | 7-T-1_2||42,296,152||51,527,101||82.1% |- | 7-T-2_1||42,767,775||52,191,210||81.9% |- | 7-T-2_2||45,814,173||57,146,402||80.2% |- | 7-T-3_1||43,288,619||53,666,959||80.7% |- | 7-T-3_2||36,712,682||44,754,376||82.0% |- | 7-T-4_1||33,329,767||45,116,118||73.9% |- | 7-T-4_2||33,219,393||41,142,529||80.7% |- | 7-T-5_1||57,347,061||69,371,414||82.7% |- | 7-T-5_2||44,318,977||54,673,022||81.1% |- | CTT-FFPE-100ng_1||43,527,498||47,409,114||91.8% |- | CTT-FFPE-100ng_2||42,796,717||46,523,502||92.0% |- | CTT-FFPE-5ng_1||17,255,895||18,600,287||92.8% |- | CTT-FFPE-5ng_2||33,184,997||36,355,026||91.3% |- | CTT-frozen-100ng_1||50,274,814||55,387,277||90.8% |- | CTT-frozen-100ng_2||55,941,976||60,903,449||91.9% |- | CTT-frozen-5ng_1||14,303,236||15,310,475||93.4% |- | CTT-frozen-5ng_2||31,206,451||34,203,612||91.2% |- | NC-P-1||22,265,516||25,002,054||89.1% |- | NC-P-2||16,284,869||19,552,139||83.3% |- | NC-P-3||27,927,900||31,201,357||89.5% |- | NC-P-5||9,532,973||12,424,591||76.7% |- | NC-P-6||13,102,631||15,423,838||85.0% |- | NC-P-7||12,679,131||15,679,757||80.9% |- | NC-P-8||13,414,256||16,259,364||82.5% |- | NC-P-9||13,445,816||15,379,652||87.4% |- | PC-P-10||7,607,573||9,433,521||80.6% |- | PC-P-1||6,363,821||7,727,128||82.4% |- | PC-P-2||13,346,408||15,069,125||88.6% |- | PC-P-3||3,151,205||4,093,467||77.0% |- | PC-P-4||6,488,210||8,658,320||74.9% |- | PC-P-5||5,347,960||6,722,768||79.5% |- | PC-P-6||6,788,449||8,497,332||79.9% |- | PC-P-7||6,294,024||8,269,872||76.1% |- | PC-P-8||4,804,772||5,698,389||84.3% |- | PC-P-9||3,845,849||4,390,032||87.6% |- | PC-T-1_1||44,275,077||53,030,360||83.5% |- | PC-T-1_2||51,315,205||59,257,668||86.6% |- | PC-T-2_1||68,245,319||80,836,193||84.4% |- | PC-T-2_2||59,886,740||67,965,891||88.1% |- | PC-T-4_1||56,814,606||65,283,928||87.0% |- | PC-T-4_2||53,207,679||61,130,443||87.0% |- | PC-T-6_1||65,535,581||77,482,439||84.6% |- | PC-T-6_2||53,192,172||63,933,657||83.2% |- | PC-T-7_1||48,504,470||56,835,764||85.3% |- | PC-T-7_2||46,509,004||55,296,800||84.1% |- | |}
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