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Cuflinks -Compare Paired Reads With Single Ended Reads

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
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updated by Biostar Biostar • written by A. Domingues A. Domingues

1 answer

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.

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written by Ido Tamir Ido Tamir

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 :)

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written by A. Domingues A. Domingues

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