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Can I generate hic without going through the whole pipeline again? #4

Open sethb3744 opened 5 years ago

sethb3744 commented 5 years ago

I already ran the MAPS pipeline and it completed successfully, but this time I would like to generate a .hic file. Is there any way to generate the .hic file without going through the entire pipeline all over again? My cluster is running out of storage space and I am having a hard time re-running the whole process again with success due to limited space. The process took 2 days last time and I've already used up 2 days waiting to see if the pipeline might be successful this time (sadly it was not).

Thanks, Seth

armenabnousi commented 5 years ago

Hi Seth, we are extremely sorry for the late response. At the time when the issue was raised there was no way to generate the hic input file without rerunning, unless by some tweaks in the code. However, we are glad to announce that the new version of the MAPS output allows for such procedure. By running "feather split" command.

Amelie-ly commented 2 years ago

Hi Seth, we are extremely sorry for the late response. At the time when the issue was raised there was no way to generate the hic input file without rerunning, unless by some tweaks in the code. However, we are glad to announce that the new version of the MAPS output allows for such procedure. By running "feather split" command. Hello,I have the same question with Seth,could you please explain the usage of command "feather split" in detail,because I can't find this command and run it now? Thanks very much!

brottodb commented 1 year ago

Hello, I am new in HiChIP analysis and I am trying to understand how to generate .hic files. After a lot of struggle I installed and ran MAPS for Arima HiChIP and I got all the outputs but not the .hic to generate contact matrix. It was generated a file ending in 'hic.input' and I used to run juicer tools pre, but no success so far. I did not get it how to use this feather split command (I am new at this) and if someone could help me would be amazing. Thanks in advance!