Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
DSN normalization henry.wood Sample Prep / Library Generation 3 11-19-2014 12:36 AM
denominator for normalization shurjo RNA Sequencing 3 09-03-2012 03:35 PM
How to Calculate RPM value for gene swapnil2188 RNA Sequencing 2 02-12-2012 08:13 AM
how to determine the RPM threshold for MeDIP zchou Bioinformatics 0 12-01-2011 01:52 AM
microRNA normalization kenosaki Bioinformatics 2 08-29-2011 08:15 PM

Thread Tools
Old 05-19-2011, 10:26 AM   #1
Location: argentina

Join Date: Apr 2011
Posts: 16
Default sRNA Normalization wiht RPM, help!

Dear Members

Im just starting my postdoctoral fellow and my new proyect involve sRNA Deep Seq. Im having problems with the data normalization.
Ive been reading papers about it and the variety of normalization method is huge!
The simplest one that I found is by TPM or RPM (transcript per millon or reads per millon), in which each raw read count is multipled by 1 millon and then divided bu the total read count of the whole library.
The question is: which library!?
I have 3 treatments. In one of them, the number of raw seq were 10 millons. After filtered of adaptor, length < 15nt, # <3 count, we generate 8 millons of mappable reads. Then, once we mapped against Arabidopsis genome, 3 libraries were generated. The mapped mRNA, tRNA, rRNA, RFAm, Repbase library (5.7 millon; 72%); the custom virus we sent library (20; 0%) and the miRNA (sRNA) library (2.3 millon; 28%). On the 3 treatments the numbers were diferent and always the miRNA library was smaller than the mRNA library.
In order to a direct compare between data set, we have to normalized the counts. If I want to do it with RPM, which library do I have to use? The total mappable reads (including mRNA, tRNA, etc) or only the miRNA library?
I have notized that the result is very different with one or the other, because the percentage of the libraries are not the same between treatments.

Any hint you can provide me will help me a lot.
Thanks in advance
dzavallo is offline   Reply With Quote
Old 10-03-2011, 08:18 AM   #2
Senior Member
Location: MA

Join Date: Oct 2010
Posts: 160


Sorry to ask you this but, have you got any answer to this question?

cascoamarillo is offline   Reply With Quote

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 10:04 AM.

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