Entering edit mode
4.1 years ago
I am trying to do motif analysis, and I just downloaded mm10 fast file from UCSC to retrieve the entire sequences of each chromosome. However, I noticed that there is a bunch of "N"s at the beginning of each sequence of chromosome. Should I remove these "N"s before I extract my sequence of interests by using BED file? Or does the counts of position of sequence include these "N"s?
Any feedbacks will be appreciated!
Motif analysis, what does that mean in detail? What are you trying to do?