Identify differentially expressed genes from single-end Vs. paired end samples

[DAnand]

Hi all,

I have two-mouse RNA-seq samples from illumina platform and I am interested in genes and their isoforms that are differentially expressed between sample1 and sample2.

Sample 1- Single-end reads X 3 replicates
Sample 2 - Paired-end reads X 3 replicates

I want to know whether it is appropriate to process sample1 and sample2 separately for Tophat ->Cufflink and merge the Cufflink-GTF-files together to perform Cuffdiff ?

I would appreciate any suggestion.

AD

[dpryan]

You should always run all of the samples separately up to the cuffdiff step.

[DAnand]

dpryan@ Thanks for the suggestion.