hickit
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lh3
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
Dear developers, thank you for creating such an exciting modelling tool. I was wondering whether it would be possible to somehow use hickit for modelling of bulk whole genome Hi-C,...
Hi, I want to use this tool to find TADs but met a problem. here is my scripts: first, I used minimap2 to mapping HiC reads to my genome: $MINIMAP/minimap2...
Hello @lh3 @tanlongzhi , I know that we can convert .con to .hic file in the dip-c repository, but Is there a way to get the genome wide contact matrix...
Hi I run into the problem as following, Can you please help with it? ``` hickit.js:457: Error: [File] Fail to open the file file = new File(args[getopt.ind]); ^ Error: [File]...
Hi @lh3 @tanlongzhi I'm a little confused that the strand for R2 was reversed here. Did I miss anything? `// read_num for PE sequencing: 1 for R1, 2 for R2 ...
Hi!, I'm attempting to convert a .pairs file to a .3gd file but am recieving the following error: ``` hickit: io.c:81: hk_parse_seg: Assertion `c != 0' failed. ./infer-3dgc.sh: line 5:...
Hi @tanlongzhi I have processed single cell data using the hickit pipeline. After phase imputation I was able to generate the 3dg file. Now that I try to convert this...
Hi Heng, Before I dig into the code, may I ask about how different it will be between bulk hic and single cell hic when use hickit to construct the...
Hi, I would like to try hickit with an allotetraploid denovo plant genome with HiC. It appears that HiC data has replicates because all my files looks this: ``` ls...
