Closed oursu closed 7 years ago
here is a picture of a larger genomic region at the same site
Hi Oana,
Thank you for brining up this interesting point to our attention. There are potentially several ways to go about this:
Additionally, Dixon et al. directionality index used to find domains has an explicit parameter of 2Mb (discussed in their Supp. material, p. 6-7) which could contribute to the results you see w/ their method.
Hope this helps and please let us know if there is anything else!
Hi, Thank you very much for all your help.
I am writing to ask for some advice on running Armatus. I have run it on my dataset consisting of 40kb window interaction counts, following normalization by ICE. I then compared the domains I got with the domains in the Dixon et al. paper, as well as the HiC input data used to call these domains (image attached). I consistently find sets of very small domains, even in places where the HiC data support a larger domain (e.g. at the region 6 000 000 - 8 000 000). I wanted to check whether you could advise me about why I am getting such a behavior, and how I could proceed.
Thank you, Oana![tads_40kb_hic_first10mb](https://cloud.githubusercontent.com/assets/5633306/5927948/7adecd44-a62b-11e4-99f7-6f76143ec47f.jpg)