Editing
Athurva Gore/LabNotes/2009-8-25
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!
{{ AGLabEntry|2009-8-24|2009-8-26 }} =ProbeSet Generation= * Currently creating TDMR set and CpGSNP set with new no-library-construction protocol * This requires a constraint of arms+target = 105 * This will allow reads of 60-80 bp (after digestion) to cover the entire fragment, greatly improving the capturing protocol (as it seems that library construction is a major source of headaches) =NA12878 False Positives= * Noticed that many misses have high number of start/end sites for reads * Checked actual read mapping; it seemed that the end of reads was causing the most trouble ** Many reads had several SNPs in the last few bases * After discussing with Dr. Zhang, decided to test mapping and SNP calling using the following protocol. ** Reads were inspected after mapping to see if any SNPs were present in bases 36-40 ** If any SNPs were present, the entire read was thrown out ** Hypothesis: Junk is getting ligated onto the ends of reads during library construction ** If we remove the junk reads, we should be able to greatly improve the false positive rate * Remapped and SNP-called the HL006 s_4 (size-selected) and s_5 (not size-selected) sets ** Filtered out clonal reads ** Removed reads that had SNPs in locations >= the 36th base * Wanted to see if false positive rate went down (though since entire reads are being rejected, coverage will decrease and therefore false negative rate will go up) * '''Results:''' ** Stored in /media/TmpStore1/AG_scratch/Exome/NA12878/HL006/noclonal/newtest ** '''POST SPECIFIC RESULTS HERE''' ** Works extremely well! ** Number of non-dbSNP calls is reduced to ~100 ** Lose ~1000 hits, but ** We only lose around 200,000 reads! ** Works extremely well. ** Will now apply it to IPS data. =IPS and Cancer= * Tested DF-6-9-9 and foreskin fibroblast non-sizeselected reads against each other (HL006, s1 and s3) * However, removed clonal reads and reads with SNPs in locations >= 36th base as above * Location: /media/TmpStore1/AG_scratch/Exome/DF-6-9-9/HL006/removeBadLig ** Running mapping/SNP calling scripts now ** Should reduce number of false positives * False positive rate was found to be greatly decreased ** '''POST SPECIFIC RESULTS HERE''' ** Only a few SNPs not at dbSNP locations compared to before ** Need to investigate thoroughly, filter out bad calls * Now running script to generate variant pairs between S3 and S1; looking for a gain of heterozygosity with particular interest
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:AGLabEntry
(
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