Julie Segueni

Thanks for your comment. Some of the reads were paired but I'm only using the R1 for everyone in this run. Should I use the R1 and R2 reads when...

ok thank you

Hi, I just read here https://github.com/arq5x/lumpy-sv/issues/110 that I can use lumpy with single-end reads. Is there a way to make that work also with smoove that uses lumpy? Best, Mas.

Hi, When plotting your heatmap, you can output the regions using the --outFileSortedRegions option. You will get an output file with the deepTools_group identifying the clusters. Best, Julie.

The other files are the expected inter and intra interactions and you can find them here for the human genome: https://salkinstitute.app.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx

Hey @musiccccc, I posted an edited version of TopDom to overcome the issue you mentioned, that I also faced in my high-resolution Hi-C matrices. You can find it here: https://github.com/JSegueni/TopDom....

Hey @Nohaosma, I also faced this issue and have posted a solution to overcome it, here: https://github.com/JSegueni/TopDom Hopefully, this can help. Best, Julie.