Output file of motif instances

Question

[rbronste]

Hi all,

Trying to output a file of motif instances in the following format:

Chr   Start     Stop      Strand  PwmScore
chr10 3944439   3944456   +       15.21570492
chr10 15627426  15627443  -       20.39377594

Anyone know a quick and easy way to do this? Thanks

[Ram]

You've got to be more specific and give us more details. For starters, what is your input dataset, what have you tried, and where exactly did you face a challenge?

[rbronste]

So I am trying to generate a motif instances file to feed into msCENTIPEDE, for any particular motif: https://github.com/rajanil/msCentipede

So far I have tried using the R version of CENTIPEDE but found this python version to be easier to use and has some extra options helpful to me such as the ATAC-seq parameter. My input dataset will just be a few BAM files from my experiments.