Cut&Run Matrix Generation


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.




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