Hello again,
I have just recently got the program PINDEL to work on my reads, and it identified a large deletion (9kb) in my region of interest (gene family, roughly 40kb). What I would really love, is to take all the reads from PINDEL, and my original alignment from that particular area, and re-align them without the reference, to see if it can make sense of the region. Has anyone had any luck doing such a thing? If so, can you point me in the right direction?
Thanks so much
A
/I've also already designed primers to test if this deletion is legit, so that's obviously a first step.
I have just recently got the program PINDEL to work on my reads, and it identified a large deletion (9kb) in my region of interest (gene family, roughly 40kb). What I would really love, is to take all the reads from PINDEL, and my original alignment from that particular area, and re-align them without the reference, to see if it can make sense of the region. Has anyone had any luck doing such a thing? If so, can you point me in the right direction?
Thanks so much
A
/I've also already designed primers to test if this deletion is legit, so that's obviously a first step.
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