Editing
Athurva Gore/LabNotes/2010-1-8
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!
=PGP= ==Estimated Mapping Rate== * Dataset mapping table (October through now): ** HL013 to HL030 {| {{table border=1}} | align="center" style="background:#f0f0f0;"|'''Flowcell''' | align="center" style="background:#f0f0f0;"|'''Lane''' | align="center" style="background:#f0f0f0;"|'''Reads Times 4''' | align="center" style="background:#f0f0f0;"|'''Number of Reads''' | align="center" style="background:#f0f0f0;"|'''Mapped Reads''' | align="center" style="background:#f0f0f0;"|'''Mapped Downsampled Reads''' | align="center" style="background:#f0f0f0;"|'''Mapping Rate''' | align="center" style="background:#f0f0f0;"|'''% Usable Reads''' |- | HL013||1||59491092||14872773||12555897||8987088||0.84||0.6 |- | HL014||6||47862784||11965696||8324230||5959697||0.7||0.5 |- | HL015||1||53717748||13429437||9839373||6031436||0.73||0.45 |- | HL019||4||59623024||14905756||8695192||8691338||0.58||0.58 |- | HL024||1||64242556||16060639||14817937||13563313||0.92||0.84 |- | HL025||1||36424692||9106173||8077318||6247035||0.89||0.69 |- | HL027||8||47824792||11956198||9269899||8819601||0.78||0.74 |- | HL028||6||37242492||9310623||5979563||4630087||0.64||0.5 |- | HL029||1||33484628||8371157||3396996||3355959||0.41||0.4 |- | HL030||1||58820868||14705217||8827261||8492613||0.6||0.58 |- | AL006||5||57942248||14485562||10565704||9604607||0.73||0.66 |- |} ==Estimated Number of Reads Usable== * We can use this to predict how many usable reads we have for each data set. ** Count of reads for each PGP sample: {| {{table border=1}} | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Reads''' | align="center" style="background:#f0f0f0;"|'''Estimated Usable Reads''' |- | PGP1||73,656,659||58,630,458 |- | PGP2||13,777,534||8,325,274 |- | PGP3||19,642,850||12,613,974 |- | PGP4||39,022,194||21,228,150 |- | PGP5||18,620,501||12,083,551 |- | PGP6||44,542,386||23,913,315 |- | PGP7||28,619,340||17,384,463 |- | PGP8||116,237,040||63,690,701 |- | PGP9||117,277,366||60,695,633 |- | PGP10||26,108,372||13,478,483 |- |} * How much coverage will this get us? ** Map a few data sets and check? ==Test Coverage== * PGP1 is done; can merge once mapping/downsampling/slidingTrim for other sets is done * Will then start: ** PGP2 (only a few datasets; "lower end") - DONE ** PGP4 (middle of the road) - DONE * Can hopefully get an idea of "# of reads -> how much coverage at read depth 8 and quality 30" * Mapping is done, now merge all lanes for the 3 PGP flowcells into one file for each ** Then check what our coverage looks like and what our dbSNP percentage is for each case * Currently merging data =PGP Paper= =IPS and Cancer= * Finish up Nature Letter draft. ** Need to fix methods section so it sounds better. ** Need to cut down online methods by ~700 words ** Need to go over main text, make sure it still sounds ok * Then, send to Dr. Zhang by end of this weekend.
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)
Template used on this page:
Template:Table border=1
(
edit
)
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