Hi :
I'm going to try the methods of loop calling in your article https://doi.org/10.1038/s41467-019-08940-5 , and I think this method for loop calling is very useful and accurate !
First, I called loops for each resolution using juicer (5kb to 25kb, 1 kb bin-size interval) , then I combine loop calls from all resolutions using cat all_res_loop/*/merged_loops.bedpe | grep -v "#" > allres.loop , and merge loops within 20kb using pgltools formatbedpe allres.loop > allres_loop.pgl and pgltools merge -a all_loop.pgl -noH -d 20000 > merged_all_loop.pgl.
We can see the lcoation of merged loop is accurate in the picture but the size of some loop anchors are so long. I downloaded the merged loop in your article, and found the max size of these loop anchors are 60 kb. So, counld you give me some suggestions?
QianzhaoJ
commented
4 years ago
Hi : I'm going to try the methods of loop calling in your article https://doi.org/10.1038/s41467-019-08940-5 , and I think this method for loop calling is very useful and accurate ! First, I called loops for each resolution using juicer (5kb to 25kb, 1 kb bin-size interval) , then I combine loop calls from all resolutions using
cat all_res_loop/*/merged_loops.bedpe | grep -v "#" > allres.loop, and merge loops within 20kb usingpgltools formatbedpe allres.loop > allres_loop.pglandpgltools merge -a all_loop.pgl -noH -d 20000 > merged_all_loop.pgl. We can see the lcoation of merged loop is accurate in the picture but the size of some loop anchors are so long. I downloaded the merged loop in your article, and found the max size of these loop anchors are 60 kb. So, counld you give me some suggestions?Thanks in advance ! Best wishes Qianzhao