Geoff Fudenberg

would be great to update cli docs, e.g. for cooler coarsen to highlight required fields, e.g. cooler coarsen FACTOR INPUT OUTPUT and add/link to examples as well

any way to get the missing bins to export as white instead of black in the SVG? thanks! update: there seems to be an extra black polygon that is deletable...

so should be able to make square regions as an option, ie. having the diagonal of the heatmap intersect the upper left and lower right corner, which it doesn't necessarily...

I couldn't find these in the referenced posts, but it would also be nice to have: a) P(s) for different read orientations separately as well-- this is useful for for...

I was getting unintelligible errors when I tried to run libraries with some funky characters their names-- it would be great if there were some checks for those as well...

Could you try with tensorflow version 1.15? (Pip install tensorflow==1.15) Thanks! On Thu, Mar 12, 2020, 1:51 AM octolis wrote: > Hi, sorry for the long response. > I'm using...

Hi @amingc3 we used the following approach: https://gist.github.com/gfudenberg/6c3219065217d2251a9c5ce31e8596ce. If you processed all data into coolers with 5kb bins, then this could create a bed file with 5kb bins.

Distiller code for going from reads to binned contact maps can be found here: https://github.com/open2c/distiller-nf (it relies on pairtools: https://www.biorxiv.org/content/10.1101/2023.02.13.528389v1.full and cooler) We used defaults for filters, mapq30 filter for...

Yes, but for that experiment I'd just start with the .pairs file, as they were processed with distiller anyways.

Hi Yarden, cooler handles the iterative correction (ICE) and binning, we used defaults for human data-- please see the cooler docs/manuscript for more info: https://cooler.readthedocs.io/en/latest/datamodel.html, https://academic.oup.com/bioinformatics/article-abstract/36/1/311/5530598 Hope that helps!