How to calculate resolution of HiC matrix

[Shane Evans]

Hi,

I am wanting to determine the resolution of my data set. We are trying to go for 1KB, and right now it seems like all that Juicer will calculate is 5KB. I am not sure if this is because of the actual resolution of my data set or because of the way I am running the software. Is there a way to check what resolution I have reached with my current sequencing depth?

Thanks so much for all your help with everything.

Best,

-Shane

[Neva Durand]

Hello Shane,

You can give any resolution with the "-r" flag when calling Juicer Tools Pre:

-r <comma-separated list of resolutions> Only calculate specific resolutions

You can modify the call to Juicer Tools Pre within your Juicer script or just run it separately. You would need to list all the resolutions you want.

As for the depth of your experiment - we usually recommend 2 billion reads for loop-resolution maps.

There's code to determine map resolution as we did in the 2014 Cell paper here: https://github.com/aidenlab/juicer/blob/master/misc/calculate_map_resolution.sh

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Neva Cherniavsky Durand, Ph.D.

Pronouns: she, her, hers

Assistant Professor, Aiden Lab

www.aidenlab.org

[Dittman]

is the calculate_map_resolution.sh merged_nodups.txt like this? Because I used pairtools to generate the hic matrice...

#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2

A00583:870:H5JNGDSX3:1:2128:21649:29528 chr1    10611   chr1    1220428 -       +       uu      A00583:870:H5JNGDSX3:1:2128:21649:29528^Y81^Ychr1^Y10505^Y50^Y4>

A00583:870:H5JNGDSX3:1:2524:27706:24079 chr1    54841   chr1    223599838       -       -       uu      A00583:870:H5JNGDSX3:1:2524:27706:24079^Y113^Ychr1^

Neva Durand 在 2020年1月11日 星期六凌晨3:10:07 [UTC+8] 的信中寫道：

[Amina]

I am having a similar issue. Did you manage to find a solution?