jiangshan529

chimeric_sam.awk not work

1

Hello, I am using Juicer to analyze a HiC data without information on restriction enzyme. The mapping goes successfully. However, the chimeric_sam.awk does not work. Here's the error information. (-:...

conda install problem

1

Hi, Joachim, I have used 'conda create --name hicexplorer36 hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge' many times and it works fine, but today when I use it again, it is...

Hi, I use bamcoverage RPKM to normalize individual samples. Now I want to compare two different chip-seq samples by visualizing them in heatmap, is RPKM normalization to each individual sample...

Hi, Is there a parameter to get only KR normalized data to cool format? Thanks!

To access a value by position, use `ser.iloc[pos]` chroffset = self.clr.offset(region[0])

4

Hi, dear authors, I have used coolpup a lot previously, but recently it has some problem(maybe a version problem of some packages): coolpup.py aa.cool bb.bed --outname cc.txt --flank 250000 --local...

running pairtools merge sequentially produces circular dependencies

2

Hi, I am merging two .pairs.gz files, but met this problem: $ pairtools merge --max-nmerge 7 --nproc 8 --memory 100G --tmpdir ./ --output ./merge_KO.pairs.gz ./*.gz Traceback (most recent call last):...

What is 'NaN' in the third column in retreived txt files

18

Hello, I have retrieved the information from a .hic file. However, I found 'nan' values in the third column. What does this mean? Is this missing values? Why should such...

Hi, Dear team members, I am trying to use scaling method in computaMatrix to plot PRO-seq signal from TSS to TES. However, the signal in the gene body(which is the...

calculating insulation score get inconsistant results

6

Hi, I am using GENOVA to calculate insulation score. the code is hic

how to write insulation score s3 format to bedgraph format

4

As shown in the title, I would like to get a bedgraph file of insulation score. Thanks!