nsites lower than the number of sequences despite using OOPS

Joel Wallenius

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Jan 17, 2018, 9:43:28 AM1/17/18

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Hello!

I ran MEME with OOPS, and 707 sequences. For some found motifs though, the nsites value is shown to be less than 707. Sometimes it's 703, other times it's 665.

Example grep in the meme.txt output file:

meme_out_UTR5.22/meme.txt:nsites: minsites= 665 maxsites= 665 wnsites= 0.8
meme_out_UTR5.22/meme.txt:letter-probability matrix: alength= 4 w= 22 nsites= 665 E= 1.3e-074
meme_out_UTR5.22/meme.txt:letter-probability matrix: alength= 4 w= 22 nsites= 665 E= 1.1e+270
meme_out_UTR5.22/meme.txt:letter-probability matrix: alength= 4 w= 22 nsites= 665 E= 2.8e+627
meme_out_UTR5.22/meme.txt:letter-probability matrix: alength= 4 w= 22 nsites= 665 E= 2.7e+849
meme_out_UTR5.22/meme.txt:letter-probability matrix: alength= 4 w= 22 nsites= 665 E= 4.5e+993

Any idea of what is happening?

CharlesEGrant

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Jan 18, 2018, 3:29:38 PM1/18/18

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Could you forward us a copy of the full meme.txt file? That would help us troubleshoot the issue.

Charles

Joel Wallenius

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Jan 19, 2018, 6:19:50 AM1/19/18

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I would but I already removed all output and re-ran everything. I can't replicate the issue, it seems... strange. I'll holler if I encounter it again!

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