Re: MEME parallel mode for multiple motif discovery

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CharlesEGrant

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Aug 12, 2015, 6:52:43 PM8/12/15

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Hi Payman,

Was there any sort of error message when MEME failed? Would it be possible to forward us s copy of your sequence file? That would help with troubleshooting.

Note that the running time of MEME increases with the cube of the the number of sequences. A sequence file with 10,000 reads probably won't be practical to analyze with MEME, even on a multi-core machine. See MEME: Dataset size and run time issues. If the sequences are highly redundant (ChIP-Seq for example) you may want to use MEME-ChIP instead.