Hello, I am using pindel to find deletions. First, I use real data(read length is 75bp) of 10 fold of a genome in which 85% are repetitive sequences, and i find some deletions.Then, simulated data were generated to evaluate the accuracy based on a real data of 200kb.I simulated 75bp,10 fold, 20 fold,50 fold respectively, at different fold, i found different numbers of deletion of 1,13(of which, 1 is not in the right chromosome), 47(of which, 5 is not in the right chromosome ). Then my question is what do you think the least fold when using pindel to find deletion.
I saw published paper using 20X, 40X of 35bp read length,does it ok to use data of 10X at a read length of 75bp for a genome possessing 85% repetitive sequences?
Expecting to your reply!
Thanks!
jane
I saw published paper using 20X, 40X of 35bp read length,does it ok to use data of 10X at a read length of 75bp for a genome possessing 85% repetitive sequences?
Expecting to your reply!
Thanks!
jane
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