Closed khsjh closed 1 year ago
Oh, sorry for the confusion, but I changed API of Fast-Higashi over the time, and the data in that folder no longer runs. Main cause is that, before I store all chromosomes into one chunk in a pkl file, not they are chunked by chromosome to improve IO & memory usage. As for the PFC data, you can get it from the original m3c paper.
All the tutorial & notebook here stays up to date: https://github.com/ma-compbio/Higashi/wiki/Fast-Higashi-Gallery
I'm trying to run tutorial with Fast-Higashi on Lee et al. dataset (sn-m3c-seq on PFC). I downloaded all of file in goole drive (https://drive.google.com/drive/folders/1SuzqQ_9dliAmTb-fGprFnN3aZrfWS-Fg?usp=sharing)
The code that I used is below
And the error was occurred
In the tutorial description, below sentence is located "To run Fast-Higashi for a new dataset, please prepare the same input files for the Higashi software. Use the Higashi software higashi.process_data() to transform contact pair files to sparse contact maps."
Is this mean that I should use Higashi at first? But, then, I can't use FastHigashi(config_path=config, ... function because it will be substituted Higashi(config).
Why this error is occurred?