SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
mRNA fragmentation for 100bp paired-end reads amdic2 Illumina/Solexa 7 09-01-2013 05:54 AM
looking for RNA degraded data lpantano General 0 07-21-2011 09:33 AM
Using degraded RNA with TotalRNA Seq Kit pmiguel SOLiD 0 04-06-2011 06:00 AM
use bowtie for paired-end mRNA-seq reads? liux Bioinformatics 3 11-16-2010 10:18 AM
Binning of aligned mRNA-reads into gene models jwaage Bioinformatics 1 03-04-2009 05:40 AM

Reply
 
Thread Tools
Old 09-27-2010, 08:25 AM   #1
Joanne Harding
Junior Member
 
Location: London

Join Date: Sep 2010
Posts: 3
Question Which reads are degraded mRNA?

Hi all,
I have a Illumina small RNA-seq dataset. I want to know if it is possible to distinguish between a genuine small RNA and a degraded messenger RNA fragment?

The dataset has already been compared to all known small RNA databases. I thought that the percentage of reads which align to exons of known genes might give an idea. Any other ideas/thoughts much appreciated!
Joanne Harding is offline   Reply With Quote
Old 09-27-2010, 08:42 AM   #2
Lee Sam
Member
 
Location: Ann Arbor, MI

Join Date: Oct 2008
Posts: 57
Default

Hi Joanne. How about trying to align to both exons and splice junctions using short seeds and fairly tight thresholds (20mer, 1 mismatch)? You might end up with some reads that align as both small RNAs and degraded, but at least it'll give you an idea?
Lee Sam is offline   Reply With Quote
Old 09-27-2010, 11:03 AM   #3
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

Quote:
Originally Posted by Joanne Harding View Post
Hi all,
I have a Illumina small RNA-seq dataset. I want to know if it is possible to distinguish between a genuine small RNA and a degraded messenger RNA fragment?

The dataset has already been compared to all known small RNA databases. I thought that the percentage of reads which align to exons of known genes might give an idea. Any other ideas/thoughts much appreciated!
Well, that is a whole debate..

If you assume that all small RNAs that are generated by cleavage of a longer mRNA are degradation products, then i guess that quite a few (if not all) miRNAs, snoRNAs or piRNAs for instance might technically be considered as "degraded mRNA fragment"..
In fact, thousands of sRNAs are made from mRNA cleavage, can be re-capped and polyAdenylated (PMID: 19169241).

In my humble opinion, the point is not just about the generation process ("degradation" vs. "processing"), but about the function of these molecules. Yet another debate: if you believe that only the known small RNAs can be functional and not the novel ones, then it is fair to consider the difference with the current databases as a good evaluation criteria -as novel sRNAs are still being reported these days, i doubt that this is a reasonable assumption. Otherwise, unless you adopt the simplistic "weak signal is noise" philosophy, i fear there is no easy way to address your question..
steven 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 04:20 PM.


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