SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Common elements within two set of miRNAs Giorgio C Bioinformatics 1 01-05-2012 10:35 AM
PubMed: Deep sequencing of microRNA precursors reveals extensive 3' end modification. Newsbot! Literature Watch 0 08-20-2011 12:02 AM
way to normalize copy number data for small RNAs/miRNAs? vebaev Bioinformatics 2 03-28-2011 03:18 AM
Can you really see miRNAs on gels before PCR amplification fisher Illumina/Solexa 3 07-27-2010 07:37 PM
PubMed: Prediction of novel miRNAs and associated target genes in Glycine max. Newsbot! Literature Watch 0 03-05-2010 03:00 AM

Reply
 
Thread Tools
Old 08-03-2011, 01:15 AM   #1
vebaev
Senior Res.
 
Location: Plovdiv, Bulgaria

Join Date: Oct 2008
Posts: 110
Default mapping reads to known miRNAs precursors

Dear all,
I'm trying to estimate the all reads count that are mapped to a specific precursor. I have done it my using bowtie with no mistmaches -v 0
But in some papers and tools I see that thay allowed 1 mistmache?! I compared the results in both way. Most of the counts are similar but for some miRNAs thay are doubled like in mir143 bellow:

with 1 mistmach mapping:
miR-143 - 4,697,060
miR-10b - 520,833

with 0 mistmach mapping:
mir-143 - 1,976,574
mir-10b - 501,099

So which is the right way? I thought it should be with 0 mistmaches since non specific tags can align when mistmaches occure but some people do it? And if I want to estimate diff.expression I should know which method is most relevant?

Thanks
vebaev is offline   Reply With Quote
Old 08-03-2011, 06:48 AM   #2
DZhang
Senior Member
 
Location: East Coast, US

Join Date: Jun 2010
Posts: 177
Default

vebaev,

a straightforward way to check is to look at the alignments in any genomics viewer. It will tell you exactly which base(s) are not perfectly aligned for these genes. I believe some people allow one mismatch to accommodate sequencing errors or SNPs.
DZhang 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 08:49 AM.


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