SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffdiff output different FPKM if the comparing samples are different rossini Bioinformatics 5 03-25-2013 04:51 AM
Comparing Samples with 20Mbp coverage to 40MBP coverage sgoswami RNA Sequencing 0 03-09-2012 07:41 AM
Marking duplicates and comparing 2 WE samples? angerusso Bioinformatics 0 02-19-2012 05:04 PM
comparing samples with varying no. of reads for differential expression harshinamdar Bioinformatics 1 08-24-2011 05:16 AM
RNA-seq pair-end normalization between samples, FPKM from cufflinks 1.0.3 fabrice Bioinformatics 0 07-21-2011 03:24 AM

Reply
 
Thread Tools
Old 11-14-2012, 10:36 AM   #1
jk1124
Member
 
Location: U.S.

Join Date: Oct 2012
Posts: 17
Default Comparing FPKM across samples

I have two RNA-Seq samples, one which I performed using Spike-In Controls and the other without Spike-Ins.

I mapped and assembled (Tophat, Cufflinks) the first using a reference assembly (-G option, no novel) and bowtie index with spike-ins concatenated to the end. The other I mapped and assembled using a reference assembly (-G option again, no novel) and bowtie index without spike-ins concatenated to the end.

Can I compare the FPKMs I get from each assembly?

Or I could perhaps reassemble my first sample using the reference assembly without Spike-Ins, and provide the mask-file option with the Spike-In transcriptome annotation, so that the Spike-Ins get discarded. Would that work?

I would appreciate any insight. I am new at this.
jk1124 is offline   Reply With Quote
Old 11-14-2012, 04:12 PM   #2
jk1124
Member
 
Location: U.S.

Join Date: Oct 2012
Posts: 17
Default

Alternatively, might be a better idea to use a count based method instead?
jk1124 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 05:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO