Using HiC-Pro to analyze Micro-C data

[Nadya Fursova]

Good evening,

I am trying to use HiC-Pro to analyze Micro-C data. I found that I should omit Genome Fragment and Ligation site parameters to do this. However, I am not sure whether this means commenting out the corresponding lines in the config file or providing empty value for these variables. I have tried both options and I get no ValidPairs files generate in my hic_results/data folder (in fact the folder itself is not generated). In both cases, the HiC-Pro pipeline has stopped after plotting only one quality check plot at the "merge chunks from the same sample" step, please find the log below. I am not sure if this is actually related to not specifying the genome fragment and ligation site parameters, but this is my best guess. I would really appreciate your help to figure out what you think could be an issue here and also if you have any general advice on the parameters or any specifics of analyzing Micro-C data using HiC-Pro that you could share.

Run HiC-Pro 3.1.0
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Thu Jan  6 20:16:06 EST 2022
Pairing of R1 and R2 tags ...
Logs: logs/Control/mergeSAM.log
Logs: logs/Treated/mergeSAM.log

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Thu Jan  6 22:13:54 EST 2022
Assign alignments to restriction fragments ...

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Thu Jan  6 22:13:54 EST 2022
Run quality checks for all samples ...
Logs: logs/Control/make_Rplots.log
Logs: logs/Treated/make_Rplots.log

--------------------------------------------
Thu Jan  6 22:13:57 EST 2022
Merge chunks from the same sample ...
find: 'hic_results/data/': No such file or directory
make: *** [/usr/local/bin/HiC-Pro_3.1.0/bin/../scripts//Makefile:160: merge_valid_interactions] Error 1

Best wishes,

Nadya

[nservant]

Hi Nadya,

Did you fix your issue ?

N