aryeelab
Hichipper with HiCUP input
Hello Caleb,
We are interested in running hichipper on our HiChIP data. However, your pipelines (Hi-C, capture HiC and HiChIP) are based on HiCUP which results in a bam that contains all the Valid reads. Is it possible to use hichipper with HiCUP? If you can think of a quick fix then I can help edit the code for our internal version to include hichipper in our institute's workflow.
Thanks! Rola
Hi Rola,
Yes, I've been meaning to expand-- this seems straightforward enough.
Could you possibly provide a sample .bam file of say chromosome 22 (human) OR chromosome 19 (mouse) from HiCUP that I could test this on? I'll also work on fixing up the enhancement that was noted on the previous issue. Thanks!
Hello Caleb,
I have a downsampled example with 2 million reads from human public data if that works. I cant seem to be able to attach it anywhere ("format not supported" it says); can I send it by email?