How can I obtain genome-wide coordinates for the motif of a particular transcription factor?

Question

[Spencer]

For example,i want to plot reads distribution around TBP motif (TATAWAWR), but i don't know these motif coordinates ,how can i get it? Thanks.

[GenoMax]

See: How Do I Search A Genome For A Known Motif, And Get An Interval File Of All Instances Of The Motif?

[ATpoint]

Be aware that when scanning the entire genome you will get excessive hits simply by chance. Maybe filtering for open chromatin regions (or something else to narrow down meaningful binding sites) would help here.

[Spencer]

it helped a lot ,thanks!

Answer 1

[Alex Reynolds]

I have an answer on using FIMO, which may be of generic interest:

https://bioinformatics.stackexchange.com/a/2491/776

Not sure what TF database TATAWAWR is from, but if you have your own (MEME-formatted) PWM for that TF, you could use that with FIMO to get all hits of your TF at your desired statistical threshold.