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

enter image description here such like this

chip-seq sequence
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updated by Devon Ryan Devon Ryan • written by qingchun98 • qingchun98

1 answer

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.
• 1 views • link
written by Devon Ryan Devon Ryan

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

• 1 views • link
written by qingchun98 • qingchun98

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

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written by Devon Ryan Devon Ryan

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