SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat uniquely mapped reads mrfox Bioinformatics 2 05-23-2013 05:58 AM
How to get uniquely mapped reads from Tophat subeet Bioinformatics 10 11-28-2012 05:56 AM
not uniquely mapped reads unidodo RNA Sequencing 2 04-22-2011 02:07 PM
Uniquely mapped reads with bowtie mapper Bioinformatics 2 11-22-2010 10:44 PM
BWA Uniquely Mapped Reads NF_seq Bioinformatics 0 09-06-2010 03:32 AM

Reply
 
Thread Tools
Old 05-07-2010, 06:40 AM   #1
clariet
Member
 
Location: NJ

Join Date: Mar 2010
Posts: 18
Default cufflinks and non-uniquely mapped reads

Cufflinks appear to take not only uniquely mapped reads. I only filtered out low quality mapped reads and ran cufflinks without any problem. But how cufflinks take care of those reads mapped to multiple regions? Does it only pick the region with highest mapping score? Anyone has ideas?

I am wondering how the results will differ if I use uniquely mapped reads only.

Any input will be highly appreciated.
Clariet
clariet is offline   Reply With Quote
Old 05-08-2010, 11:13 AM   #2
lpachter
Member
 
Location: Berkeley, cA

Join Date: Feb 2010
Posts: 40
Default

The correct way to deal with reads that map to multiple places is explained in the paper by Li et al:
http://bioinformatics.oxfordjournals...tract/26/4/493

Mathematically, the ambiguity that arises from multiple hits in alignment, is no different than the ambiguity that arises when reads can belong to multiple isoforms at one location- in fact the statistical deconvolution is identical.

We plan to extend Cufflinks to correctly solve this problem in the near future.
Currently, multiple hits are assigned equal probabilities- details are in the supplement to the Cufflinks paper:
http://www.nature.com/nbt/journal/va...bt.1621-S1.pdf
lpachter is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO