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Old 05-29-2015, 07:07 AM   #1
ccpan
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Default Convert single-end data to paired-end

Hi, everybody,

I got single-end read data of RNAseq. Is there any software program that could convert single-end data into paired-end data so that I could use Chimerascan or other fusion-searching programs which only accept paired-end data?

Thanks a lot.

Camillo
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Old 05-29-2015, 07:33 AM   #2
Bukowski
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No, because the whole point of having paired end data for something like fusion detection relies on you having sequenced both ends of the same molecule.

You'd need to use a split-read approach.
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Old 05-29-2015, 10:08 AM   #3
Brian Bushnell
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Actually, I have a tool for this purpose, bundled with BBMap. Usage:

bbfakereads.sh in=singles.fq out1=r1.fq out2=r2.fq overlap=0

This will generate paired reads from single-ended reads by cutting them in half. I have used it effectively for finding chimeras by mapping.
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