Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Hi:
I tried to run merge-filter.sh for merging spatially close, significant interactions from FitHiC2, but I am confused about the output files of merge-filter.sh .
There are many columns, like chr1 mid1 chr2 mid2 and bin1_low bin1_high bin2_low bin2_high, in output files of merge-filter.sh , which one is the location of merged interactions ? And, about the parameter "fdr", do you have any recommended settings? I found there are too many merged interactions(about more than 200000 rows) if I set "fdr" to 0.01.
Thanks in advance !
Best wishes
Qianzhao
Hi: I tried to run
merge-filter.shfor merging spatially close, significant interactions from FitHiC2, but I am confused about the output files of merge-filter.sh . There are many columns, likechr1 mid1 chr2 mid2andbin1_low bin1_high bin2_low bin2_high, in output files of merge-filter.sh , which one is the location of merged interactions ? And, about the parameter "fdr", do you have any recommended settings? I found there are too many merged interactions(about more than 200000 rows) if I set "fdr" to 0.01. Thanks in advance ! Best wishes Qianzhao