how can i get or calculate the motif percentage of each sequence?

Question

[qingchun98]

such like this

Answer 1

[Devon Ryan]

This isn't plotting a motif percentage per sequence, it's the percentage of peaks containing a given motif.

1. Call peaks
2. Sort them by a score of some sort
3. Intersect with the known motif locations (i.e., annotate each peak according to whether it overlaps with the motif).
4. Load that into R, write a little function to summarize % peaks with motif in the first n peaks from that and plot.

[qingchun98]

can I use the p-value or q-value in MAST result ?

[Devon Ryan]

You can use anything you want for the ranking/sorting.