Question about arrowhead for contact domain

[dangd...@163.com]

Hello，

      I was wondering if there is a way to increase the number of domains called by arrowhead. I make sure that at least 80% rows of the matrix have more than 1000 contacts at 10k resolution. 

      I generated a hicfile and used the arrowhead to get contact domains. However, when I set the parameters : -m 2000 -r 10000 -k KR  ,  I only got 1680 domains in the whole genome,

when use the juicebox to visualize the them .  It seems like there should be many more domains but the arrowhead method didn't get them .

      Thus, I wonder how to tune the parameter to get more contact domains.

Any advice on how to increase the number of domains would be much appreciated.

Thanks,

Dachang

[Muhammad Saad Shamim]

Hey Dachang,

Have you tried running Arrowhead on the mapq0 hic map?

Best,

- Muhammad Saad Shamim

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[dangd...@163.com]

Hi Shamim,

   

    My hic map is built on mapq0. And I tried to use parameters :  -m 2000 -r 25000 -k KR, and then got 4007 contact domain. 

    So, I want to know why would this happen. I guess it's related to the contacts in the Hi-C map and the parameter for domain calling, such as s the  thresholds of sign and varience.

So I can change the -r paramter to tune the contacts in the map but how can I tune the parameters for domain calling?

    Besides,  what's the relationship of the contact domain called in different resolution ( different parameter  -r  ) and how to choose a suitable resolution to call contact domains?

Best,

Dachang

在 2018年7月14日星期六 UTC+8上午1:11:09，Muhammad Shamim写道：