SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Removing duplicates is it really necessary? foxyg Bioinformatics 34 12-02-2016 02:17 PM
Removing Duplicates Scenario Exome Resequencing Hkins552 Bioinformatics 1 12-05-2011 06:23 PM
Small RNA data analysis asaleh SOLiD 2 06-23-2011 02:04 PM
initial amount of total RNA or enriched small rna for small rna seq Deli Çoban Sample Prep / Library Generation 4 06-04-2011 04:47 PM
Small RNA data analysis katussa10 De novo discovery 2 05-23-2011 08:00 AM

Reply
 
Thread Tools
Old 07-03-2011, 10:54 PM   #1
Kennels
Senior Member
 
Location: Sydney

Join Date: Feb 2011
Posts: 149
Default removing duplicates in small (si)RNA data

Hello,

I hopefully have found most of the threads regarding duplicate removal in this forum.
(e.g. http://seqanswers.com/forums/showthr...uplicate+reads)

I am wondering if anyone has some input regarding this topic on small RNA data sets - how large an effect (if any) does real PCR duplicates have on real sRNA reads?
An sRNA read distribution profile typically displays many reads originating from an exact 5' position, which can be observed as 'hotspots' of read stacks across a reference.

I am analyzing miRNA/siRNA distribution profiles on viral genomes and hpRNAs, so the read depth is typically very high in very localized hotspots, but I am wondering if duplicates should be considered in my analysis, and if so, how does one distinguish real from duplicates reads?

thanks
Kennels is offline   Reply With Quote
Old 02-29-2012, 10:03 PM   #2
ron128
Member
 
Location: Mumbai

Join Date: Sep 2011
Posts: 38
Default

Hello. There is no real way to differentiate between pcr duplicates and "real" reads. The only way out is if you use tags in the sample preparation. We had tried something similar to what kcarr has suggested, and were able to differentiate between the two.

Duplicates IMHO would not matter much in your case unless you are studying rnaseq data or analysing expression profiles.
ron128 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 11:41 AM.


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