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jsxlei / SCALE

Single-cell ATAC-seq analysis via Latent feature Extraction
MIT License
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Problems with loading data #8

Open vswarup opened 4 years ago

vswarup commented 4 years ago

I was able to install all the dependencies correctly and running the command as SCALE.py --help works fine. I am using python 3.7.3 and Ubuntu 18.04.3. I am trying to use my own data as the tutorial data keeps failing to download. I suspect that the data is not in the right format, see attached screenshots.

Screen Shot 2019-10-25 at 4 10 26 PM Screen Shot 2019-10-25 at 4 12 06 PM
jsxlei commented 4 years ago

Your three files's format is correct. It seem that your mtx file contains unknown char b'8\x1047', remove this may work. You can try to use the scipy.io.mmread function to read mtx file to check whether it is in right state.