[miso-users] Motif location

[Yarden Katz]

I think this was meant for a different mailing list...

  --Yarden


On Mar 4, 2014, at 2:50 PM, Delong, Zhou wrote:

> Hello,
> I reported a bug several weeks ago that when trying locating a motif within a list of genome positions, the order of input can change the result (and thus the result is not correct except for the last line of input). 
> I noticed your update and apparently the bug is not fixed.
> Here is the bug:
> Run these commands with the latest version of miso:
> 
> annotatePeaks.pl test_position_1.txt hg19 -m motif1.motif >test_output_1.txt
> annotatePeaks.pl test_position_2.txt hg19 -m motif1.motif >test_output_2.txt
> 
> with the test_position files and motif file in the attachment. Results of my run are also attached.
> 
> Notice that the two position files are the same except the order of the two lines, but the output files do not agree with each other, with a shift of 4 bp in each case.
> 
> I verified the results by hand. If my calculation is correct, the miso output is correct only for the last line of input. Thus when you use miso to locate a motif with a large dataset, most of the results are wrong.
> 
> I wonder if anybody else is trying the same thing and if they can confirm this.
> Best,
> Delong<test_output_1.txt><test_output_2.txt><test_position_1.txt><test_position_2.txt><motif1.motif>_______________________________________________
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--
Yarden Katz <yarden at mit.edu>