HiCLift

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liftover error from mm9 to mm10

1

YuhePei

Dear XiaoTao, I am trying to convert from cool to hic. Command used : HiCLift --input hiC/GSE116862_50k_sum.cool --input-format cooler --out-pre GSE116862_sum --output-format hic --in-assembly hg19 --out-assembly hg19 --out-chromsizes hiC/hg19.chrom.sizes But...

Saranya-Balachandran

Hello! I'm attempting to convert the format from Hi-C (Juicer output) to Cooler using HiCLift: HiCLift --input inter_30.hic --input-format juicer --out-pre CN-10 --output-format cooler --out-chromsizes sizes.genome --in-assembly hg38 --out-assembly hg38...

Luzmist

How to draw a beautiful HIC map

5

Hello, Professor Wang, thank you for providing so much useful software. I tried a lot of software, such as fanc,hicexplorer, but did not draw the hic map I wanted. I...

songxh1996

Dear Professor Wang, I would like to express my appreciation for your invaluable contribution in developing the tool, which has significantly facilitated my research endeavors. While utilizing the tool, I...

Gemma-Zhang-326

File doesn't have the given chr_chr map

1

Hi. When I use the following command to convert a hg19 `.hic` file to a hg38 `.cool` file: ``` HiCLift --input $INPUT --input-format juicer \ --out-pre $OUT_PREFIX --output-format cool \...

yizhang-zoey

subprocess.CalledProcessError: Command 'pairix /home/zjin/neat1/13.TAD_boundary_pile_up/mcool/.HiCLift/c2c12.pairs.gz' returned non-zero exit status 127.

1

Hi！ I am facing an issuea bout the output format. when i use the pairs ,it's ok.  but when i use the hic ,It shows an error like subprocess.CalledProcessError:...

gavinjzg

Output as .cool format instead of .mcool

2

Hi, Thank you very much for the development of this tool. I am facing an issue regarding the output format. Here is the cmd line which I used: HiCLift --input...

mb6434

AttributeError: module 'numpy' has no attribute 'object'

4

Hi Dr. Wang, I tried to convert a hg19 .hic into hg38 .hic by command line below and faced an error: pairLiftOver --input /RPE-1_HiC/GSE71831_RPE1-WT.hic --input-format juicer --out-pre test-hg38 --output-format hic...

timothykoala

Error when running pairLiftOver

1

Hi, when I run pairLiftOver I keep on getting the error: TypeError: expected str, bytes or os.PathLike object, not NoneType The code I am running is as follows: `pairLiftOver --input...

ljharrison1