HiNT
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parklab
HiC for copy Number variation and Translocation detection
Hi, I tried to run hint cnv and got these error messages. open: No such file or directory Traceback (most recent call last): File "/data2/home/song7602/Tools/HiNT/bin/hint", line 202, in main() File...
Hello, Thank you so much for all of your hard work developing this wonderful tool! I have run HiNT successfully on the test data provided (hg19), but encountered the following...
for example, if we use `-n HiC_K562` as prefix name. The string parsers may get wrong results. like ~~~ chrompair = paste(strsplit(matrix,'_')[[1]][2],strsplit(matrix,'_')[[1]][3],sep="_") ~~~ in externalScripts/getBreakPoints2steps.R
I am curious that I can get background matrix for the reference, mRatNor1, https://vgp.github.io/genomeark/Rattus_norvegicus/ Can I make background matrix myself?
hello, I want to run hint tl for other species , Is background matrices necessary ?
Hi, I tried to use your docker on coolers files: ``` $ hint tl -m out/wtg2nolabelfc1_1000kb.cool,out/wtg2nolabelfc1_100kb.cool --chimeric out/wtg2nolabelfc1_chimeric.sorted.pairsam.gz --refdir data/hg19_SNPs --backdir backgroundMatrices/hg19 --ppath /miniconda3/bin/pairix -f cooler -g hg19 -n test...
Hi, Dear HiNT developer, Thanks for developing this HiNT. I have successfully installed HiNT. I am using hint tl. But it always return ERROR: path to the matrixfile is not...
Hi, I tried to install the HiNT package using conda. But I got the following error message: ``` aaa@aaa:~$ conda install hint Collecting package metadata (current_repodata.json): done Solving environment: failed...
Hi, any chance you could reset the links of the supplementary files so that they can be access? Thanks.
Hi Park lab, I'll start by saying thanks for all the work put into this package and having it support a bunch of input file formats. That's really great and...
