I'm confused on how to generate the cut matrix for the Cut&Run experiment. I found this on one of the papers online:
Cut matrix generation For any motif of interest, its corresponding cut matrix was generated as follows. The rows of the cut matrix are the motif sites. The columns are the individual nucleotides in the − 100-bp motif and + 100-bp regions. Cut matrix requires all motif sites to be in a consistent orientation. That is, if the motif occurrence is located on the minus strand in the reference genome, all the cut frequencies in that motif site are flipped, so that − 100-bp position from the old profile becomes the + 100-bp position in the new profile. By convention, a value at ith nucleotide means the cut is situated just before ith nucleotide. The cut matrix tabulates the frequency of fragments ending in each nucleotide. To compute strand-specific cut matrix, the ends of DNA fragments that overlap with the motif were assigned to forward and reverse strand cut matrices as follows. For each fragment, define R1 and R2 as two mates. The ends of the fragment are the start of R1 (s1) and the end of R2 (e2). If a given motif occurrence appears on the positive strand of the reference genome, then s1 belongs to the “forward” strand cut and e2 belongs to the “reverse” strand cut. Otherwise, if the motif occurrence is on the negative strand, then s1 belongs to the “reverse” strand cut and e2 belongs to the “forward” strand cut. Likewise, tabulation was repeated for all paired reads and for all motif occurrences, each time separately for each strand.
Can some one please elaborate? Or give an example. Figures are appreciated.