MEME-ChiP for 50bp sequences

[ndcu...@gmail.com]

Hi everyone,

It's mentioned in the paper Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets", Bioinformatics, 2712, 1696-1697, 2011. that "The uploaded regions should be FASTA-formatted sequences of at least 100bp in length, each centered on a ChIP-seq tag peak". So I wondered if it's OK to use MEME-ChIP to do Motif discovery and Motif enrichment analyses for 50bp sequences, which are Systematic evolution of ligands by exponential enrichment (SELEX) libraries? If not, could anyone advise me where I should do the analyses?

Thank you.

Cheers,

Cuong

[James Johnson]

I discussed this with Tim Bailey and we believe that MEME-ChIP should still be useful for the MEME and DREME component as well as the automatic clustering. Our brief experiments show that it won't crash at least. :-)

The main problem with short (< 200bp) sequences is that CentriMo needs longer sequences to create an negative set and so with only 50bp it will not find anything with a significant E-value. SpaMo will also fail to work for similar reasons.

[ndcu...@gmail.com]

Thank you James for your reply :) Luckily, MEME and DREME outputs are most important for me :)

By the way, I wanted to report issues with the new MEME Suite 4.10.1. I did a couple of runs on MEME-ChIP ~ 85 hours ago and the jobs are still running, e.g: http://meme-suite.org/info/status?service=MEMECHIP&id=appMEMECHIP_4.10.114291970309961414154640. I did the same runs on the old MEME 4.10.0, and the jobs finished in ~ 3 hours. So, is there something wrong with the 4.10.0 or the server is currently overloaded?

Cheers,

Cuong

[James Johnson]

The new server had a 2 hour timeout set on the computations which caused problems with the 5 hour limit set on the MEME-ChIP script. Basically the process was being stopped before it had a chance to report the result... While it might look like they are still running that is incorrect.

We have updated the server time limit to be larger than the script limit so it should now correctly report a result. Please restart all your jobs that have been going for longer than 5 hours as they will have been stopped.

[ndcu...@gmail.com]

Thanks James :)