Hello,
I work on Pacbio Isoseq data, on A. thalina genome. I need to find the fusion transcripts and the break point of the fusion. I used the SQANTI3 pipeline to detect them : it needs a alignment step with minimap2 , without secondary alignements .
Also, I would like to get the break point (where there is the "link") in these fusion transcripts. It is not implemented yet with these tools.
Do you know a tool which could solve that problem, or do you have an idea?
I thought If I create a sliding window (n=1000nt for example) at the beginning and at the end of the fasta sequence of these transcripts with a python script.
So I will have, for example, a sliding window which creates the fasta sequences (1st nt->1000th nt , 2nd nt ->1001th nt ...) at the beginning, and same way for the end (last nt -1000nt -> last nt , last nt -1001nt -> last nt -1nt) etc.
Then, I blast these window sequences (the target should be different for the beginning and the ending sequences) and I get the breaking point where the beginning target becomes the ending target, and vice versa.
Any help?
