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Thursday, October 2, 2008

Paired End Chip-Seq

Ok, time for another editorial on ChIP-Seq and a very related topic. Paired-End Tags.

When I first heard about Paired End Tags (PETs), I thought they'd be the solution to all of our worries for ChIP-Seq. You'd be able to more accurately pin-point the ends of each fragment, and thus bracket binding sites more easily.

Having played with them for a bit, I'm not realy sure that's the case. I don't think they do any better than the adaptive or triangle distributions that I've been using for a while, and I don't think it really matters where that other end is, in the grand scheme of things. The peaks don't seem to dramatically shift anywhere they wouldn't be otherwise, and the resolution doesn't seem to change dramatically.

I guess I just don't see much use in using them.

Of course, what I haven't had the chance to do is run a direct PET against a SET library to see how they compete head to head. (I've only played with the stats for each individually, so take my comments with a grain of salt.)

That said, people will start using PET for ChIP-Seq, despite the increased cost and slightly smaller number of tags. The theory goes that the number of mappable tags will increase slightly to compensate for the smaller number of tags.

That increase in mappable tags may, in fact, be the one redeeming factor here. If the background noise turns out to be full of tags that are better mapped with their paired end mate, then noise decreases, and signal increases - and that WOULD be an advantage.

Anyhow, if anyone really has the data (SET + PET for one ChIP-Seq) to do this study, FindPeaks 3.2 now has PET support, and all the tools for doing PET work. All that's left is to get the manual together. A work in progress, which I'd be willing to accellerate if I knew someone was using it.



Anonymous Ola said...


thanks for the update on paired ends. What you could do is randomly select one of the ends of each PE fragmets as a SET library and compare it to the full PET library. I am not familiar with PET sequencing, do you get similar numbers of fragments or similar number of total reads (F+R)?

I guess another advantage would be that you know the actual number of fragments in a peak, wich would perhaps give a better correlation with the enrichment.

October 3, 2008 4:29:00 AM PDT  
Blogger Anthony said...

You're right - I had talked myself out of trying that before, but there really isn't a reason for it not to work.

I'll see if I can find a library and align it both PET and SET.


October 3, 2008 8:55:00 AM PDT  

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