hicmaptools -sites options

[Lucas446]

Hi,

I would like to calculate the interaction between all the possible pairs from a list of region in a bed file: chr start end

I use the following command:

hicmaptools -in_hic ${m} -in_hic_norm KR -in_hic_resol 25000 -sites ${bed} -random 1000 -output ${output_path}.tsv

However when I look at the results, I can see that each of the region has been paired with only 91 other regions whereas the bed file contains 234 region. Do you know how to make it look at all possible pairs ?

Thanks a lot, Best,

[jmchangTW]

Dear Lucas,

I suppose the issue is resolved since I received the following reply from you. If no other issue, I will close the issue.

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Sorry actually it is fine, the regions I input are spread among different chromosomes and I see that hicmaptools look at intra-chr interaction only not inter-chr,

I think that is it,

Best

[Lucas446]

Hi Chang,

Actually, is there a possibility to also output the interaction having 0 contacts when using -sites option ?

thanks a lot, Best, Tanguy

[jmchangTW]

Dear Tanguy,

Yes, the HiCmapTools does not print anything if no correlated bin has been found by the following if-else condition.

        // output result only there is bin count
        if(sum_bin > 0)

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Is it fine to output zeros for all metrics?

Best, Jia-Ming

[jmchangTW]

Dear Tanguy,

I mean zero for metrics sum*, rand, divide_, and rank_*. https://hicmaptools.readthedocs.io/en/latest/format.html#output

Best, Jia-Ming

[jmchangTW]

Dear Tanguy,

I have revised HiCmapTools, which will output zeros when 0 contacts happen.

Best, Jia-Ming