cooler supporting 5C data

@nvictus what is the current state of the support for the 5C type of data in cooler? Is the 5C support on the cooler development roadmap?

My understanding of the problem is limited at the moment, but @betulakgol PhD student in the Lab is trying to find workarounds to make 5C data work with cooler and eventually HiGlass. From our perspective it seems like supporting gaps in bins-layout has the highest priority for now … Such that list of bins like that is a valid bin-layout:

chr1	30000	45000
chr1	45000	60000
chr1	60000	75000
chr1	75000	90000
chr1	90000	105000
chr1	183000	198000
chr1	198000	213000
chr1	213000	228000

Given the 5C experiment was done on regions chr1:30000-90000 and then chr1:183000-228000.

Just in case, this is a collection of issues that seems related to application of cooler to 5C type of data: https://github.com/mirnylab/cooler/issues/98 https://github.com/mirnylab/cooler/issues/84 https://github.com/mirnylab/cooler/issues/81 https://github.com/mirnylab/cooler/issues/80

[betulakgol]

It worked. Thank you very much for your help!

Best, Betul

2018-06-04 19:01 GMT-04:00 Nezar Abdennur [e-mail]:

Hi Betul,

It looks like all your regions are there, they just aren’t where you expect. It’s because currently the chrom sizes you use in the cooler need to match what higlass expects, or else you need to upload a different coordinate system to higlass and use it instead.

Try reloading your coolers with this https://raw.githubusercontent.com/pkerpedjiev/negspy/master/negspy/data/hg19/chromSizes.tsv chromsizes file. e.g.

cooler dump --join .cool | cooler load -f bg2 --count-as-float hg19.chrom.sizes:1875 - <output>.cool

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[nvictus]

Hi Betul,

It looks like all your regions are there, they just aren’t where you expect. It’s because currently the chrom sizes you use in the cooler need to match what higlass expects, or else you need to upload a different coordinate system to higlass and use it instead.

Try reloading your coolers with this chromsizes file. e.g.

cooler dump --join <input>.cool | cooler load -f bg2 --count-as-float hg19.chrom.sizes:1875 - <output>.cool