I am dealing with a a hybrid sequence that came from two reference sequences, I am considering illumine paired-end sequencing to find the junction point between these two sequences in the hybrid one. My question is how to calculate the probability of the reads that will span the junction point (the point on the hybrid seq where the two ref. seq have joined, or half of each of them have joined to create the hybrid one?
The length of the sequence is 7500
The length of the two ref seq. is 7500 for each.
The fragment length is 300
The read length is 72
The window that i am interested to find the junction point in is about 1.8kb .
Many thanks
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