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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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Invalid interval bounds with chr prefix already #42

Closed zzhoujialu closed 1 year ago

zzhoujialu commented 1 year ago

Hi, thank you for developing this amazing tool. I'm trying to run calculate-cnv on a 50kb cool matrix after running the script of add_prefix_to_cool.py and I still come across the error exactly like the issue #1.

The following is the ginteractions file transforming from my cool file using hicexplorer. 截屏2023-02-07 16 17 41 My command line is: calculate-cnv -H /path/to/my/mcool/file::resolutions/50000 -g hg38 -e HindIII --output file.CNV-profile.bedGraph

Do you have any idea of what could be causing the error? Looking forward to hearing from you. Thanks!

XiaoTaoWang commented 1 year ago

Hi, this error may happen if your cool file includes chromosomes other than chr1, chr2, ..., chrX, chrY, and chrM. Can you show me all possible chromosome names in your cool file?

zzhoujialu commented 1 year ago

Thank you! There are much more chromosomes other than chr1, chr2, ..., chrX, chrY, and chrM in my cool file. I removed them and it works. Thank you so much!