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slowkow / CENTIPEDE.tutorial

:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
https://slowkow.github.io/CENTIPEDE.tutorial
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Shifted forward and reverse dip #4

Closed alexg9010 closed 8 years ago

alexg9010 commented 8 years ago

Hi,

First of all this introduction you wrote helped me a lot to understand the data required for use with centipede!

I currently using your package for my master's thesis and now i have a problem where you might be able to help me.

As you might see in the plot below the significant dip in dnase-cut probability does not overlap in forward and reverse strand. And i think this shift happened in the centipede_data function in your package.

My read length is 35 and that seems to have something to do with the shift.

Maybe you could help me to resolve this problem.

sp4_full

Thanks in advance Alex

slowkow commented 8 years ago

Thanks for opening this issue! I'd like to help you resolve this. I also noticed this strange shift in my own plot. The blue line is shifted to the right, relative to the red line. This is similar to your plot.

image

I wonder if I have a bug in the centipede_data() function. I'll try to have a look at the code in the next few days or weeks, but I need some time. I'd be very happy to review and accept a pull request about this!

alexg9010 commented 8 years ago

made up a pull request