Cuflinks -Compare Paired Reads With Single Ended Reads

Question

[A. Domingues]

I've downloaded RNA-seq data (Hs) from a published paper and to my surprise the control condition is PE and the 2 conditions are SE. No replicates.

They've used this data to determine differential exon usage between control vs condition 1 and control vs condition 2 using a "home-brewed" analysis after mapping. To answer the particular biological problem I am interested in, cufflinks (and cuffdiff) is ideal because it should allow me to extract exactly the information I am interested.

The question is: is it even possible to use cufflinks (+cuffdiff) to analyse control (PE) vs condition (SE)?

Thanks.

Answer 1

[Ido Tamir]

Obviously you should realign everything yourself with only the first read for the controls, if you really want to do it correctly. If you don't do this, you will get a much better estimate of splice sites for the control in comparison to the conditions.

[A. Domingues]

Thanks Ido. I thought so and in conversation with other people in the lab that sounded the most reasonable approach, but as none of us is a pure NextGen bioinformatician it felt like the blind leading the blind. So I came to the experts :)