SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
counting RNA-seq matches shuang Bioinformatics 13 01-31-2012 06:50 AM
RNA-Seq: 1, 2, 3: Counting the fingers on a chicken wing. Newsbot! Literature Watch 0 11-01-2011 02:40 AM
RNA-seq reads counting matrix doublealice Bioinformatics 2 04-19-2011 09:41 AM
Mapping and counting, small RNA seq. GA IIX alvin RNA Sequencing 0 10-08-2010 12:36 PM
RNA-Seq: RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. Newsbot! Literature Watch 0 08-07-2010 02:54 AM

Reply
 
Thread Tools
Old 12-25-2011, 08:33 AM   #1
ozs2006
Member
 
Location: rishon le zion ,israel

Join Date: May 2010
Posts: 21
Default RNA-seq reads counting: sum or max

Hi guys,
From first time I entered RNA-seq analysis, I always count the total number of reads that map to certain genomic area (with coverageBed of BEDTools or my own scripts) and then normalize with DESeq.
Recently, I was asked by a friend, why I summarize the reads and not for example take the maximum coverage as the number of RNA molecules that were in the sample.
We both know that there are biases like PCR-bias or sequencing-bias and biological more complicated mechanisms like alternative-splicing or alternative-promoter.
But who said that the sum is more robust to these biases?, my answer to him was that this is the method everybody use, but as you can see this is not a good excuse.
Is anyone ever compare, I guess sum is more robust but I'm not sure... what do you think?
Thanks in advance,
Oz Solomon
Israel
ozs2006 is offline   Reply With Quote
Reply

Tags
bias, coverage, deseq, normalization, rna-seq

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 08:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO