loops file in bed format

[Ferossitiziano]

Good evening,

I am trying to run my first test with the coolpup.py command and I was wondering what kind of information should the CH12_loops_Rao.bed file contains. Are these the coordinates of the interactions reported in the Scc1-control.10000.cool file?

coolpup.py Scc1-control.10000.cool CH12_loops_Rao.bed --nshifts 10 --unbalanced --coverage_norm --mindist 100000 --outname Ctrl_loop.txt --log WARNING

thank you,

Federico

[Phlya]

Dear Federico,

This is a file with coordinates of loops from the CH12 cell line, from Rao et al 2014 publication. This is the data that was used in the original snHi-C papers, and shows clear enrichment in zygote data. Hope this helps!

Best wishes, Ilya

[Ferossitiziano]

Dear Ilya,

thank you for your help, I was mostly wondering the format of the CH12_loops_Rao.bed file. I have now cloned the cool puppy repository and saw it is a 6 columns .bed format file.

I generated a contact matrix using HiCpro, which contains all the valid pairs of my dataset (see below). I then converted this matrix in a .cool file.

A00302:209:HNTYLDMXX:1:1101:1407:27070  chr10   8366768 -   chr18   33310142    -   104 HIC_chr10_13409 HIC_chr18_75848 37  15
A00302:209:HNTYLDMXX:1:1101:1470:9330   chr13   37410778    -   chr13   37419443    +   140 HIC_chr13_87004 HIC_chr13_87031 42  42
A00302:209:HNTYLDMXX:1:1101:1570:32706  chr10   98850582    -   chr10   118002409   +   128 HIC_chr10_237733    HIC_chr10_283362    42  42

and I was wondering how I could obtain a file similar to CH12_loops_Rao.bed by using my data.

Thank you,

Federico

[Phlya]

If you want to annotate peaks (loops) in your data, you can try cooltools call-dots. Other tools that work with cool files are mustache and chromosight (and maybe others).