SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat memory usage during "Searching for junctions via segment mapping" biznatch RNA Sequencing 9 02-18-2013 10:47 AM
Mappability or "why my mapping is biased?" polivares General 8 03-12-2011 09:48 AM
Solexa mapping - extraction of "not in Ref" reads Oxygen81 Bioinformatics 6 11-24-2010 09:18 AM
BWA sampe mapping result, what is "PROPER PAIR"? hl450 Bioinformatics 5 08-06-2010 02:26 PM
What is the difference between "maq match" and "maq map" cliff Bioinformatics 1 11-16-2009 03:13 PM

Reply
 
Thread Tools
Old 06-03-2010, 09:53 AM   #1
sdwy2008
Member
 
Location: IL

Join Date: May 2010
Posts: 10
Default Maq mapping score and "Mapping uniquely"??

When Maq is used for RNA-seq data analysis, I saw several people set (q) "Minimum mapping quality allowed for a read to be use" to be 30 as the cutoff value in %Maq pileup. Does this mean the reads after this "pileup" with q=30 are those "mapped uniquely"?

But, since "most of the repetitive reads have a mapping score of 0", why just set the q to be a value a little bit > 0 (other than 30) to discard the non-unique reads? Or in another word, what value should we set for q such that we can confidently say that we have filtered out all the non-unique mappings?

Thanks

sdwy2008 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 09:24 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO