SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Is it possible to do DE analysis on single tumor-normal pair with EdgeR? ymc RNA Sequencing 3 07-28-2013 12:52 AM
Illumina single-ended reads Rob2012 RNA Sequencing 3 02-11-2013 07:58 PM
tophat mapping of pair ended library from scriptseq caodan Bioinformatics 1 05-21-2012 05:51 AM
Exome sequencing: Illumina? SOLiD? Read length? Pair-Ended? mrfox Bioinformatics 11 01-23-2012 12:45 AM
RNAseq analysis using DESeq katussa10 Bioinformatics 9 08-29-2011 06:32 AM

Reply
 
Thread Tools
Old 08-13-2013, 10:29 PM   #1
ericfit
Junior Member
 
Location: iowa

Join Date: Jan 2011
Posts: 4
Default Can I put single and pair-ended RNAseq data together in DESeq analysis

I have RNA-seq data from Illumina GA (single-ended)and Hiseq (pair-ended). Just wonder if I could put them together in differential gene expression analysis. I know pair-end is much better than single-end in accuracy. But not sure if it is reasonable to put them together in the analysis. many thanks
ericfit is offline   Reply With Quote
Old 08-13-2013, 11:27 PM   #2
Simon Anders
Senior Member
 
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
Default

No, paired-end is not better in accuracy. At least, for simple differential expression analysis, it does not make much of a difference.

As for your question, the answer is: It depends.

Hence, please always give details on your experimental design when posting a question here,
Simon Anders is offline   Reply With Quote
Old 08-14-2013, 06:56 AM   #3
ericfit
Junior Member
 
Location: iowa

Join Date: Jan 2011
Posts: 4
Default

Thank you for reply.
I have 10 samples in treatment and 12 samples in untreatment group. In treatment, I have 5 single and 5 pair-ended samples. In untreatment, I have 8 single and 3 pair-ended samples.
Sorry, I am not the person who designed the experiment. Have no idea why they put it into such way. But I have to do the data analysis.

Many thanks.
ericfit is offline   Reply With Quote
Old 08-14-2013, 07:33 AM   #4
Simon Anders
Senior Member
 
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
Default

Well, as long as you have both platforms in both conditions, this is fine. Just treat the library type as a covariate, as in the example in the vignette. (There, we used on purpose a dataset with such a mixture of single-end and paired-end data to demonstrate how to use covariates.)
Simon Anders 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 11:15 PM.


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