Question: Cuflinks -Compare Paired Reads With Single Ended Reads
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gravatar for A. Domingues
6.8 years ago by
A. Domingues2.0k
Mainz, Germany
A. Domingues2.0k wrote:

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.

cufflinks cuffdiff • 1.7k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 6.8 years ago by A. Domingues2.0k
0
gravatar for Ido Tamir
6.8 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

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.

ADD COMMENTlink written 6.8 years ago by Ido Tamir5.0k

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 :)

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by A. Domingues2.0k
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