[miso-users] Motif location

[Delong, Zhou]

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
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