Error in Generating Methylation Count Matrices

[keyingkuang]

Dear EpiScanpy team,

I am having trouble using episcanpy's ct.build_count_mtx() function. I strictly followed the tutorial and used the test datasets given to build the count matrices but found that there was no output files even the code chunk ran successfully. If setting the outout_file to "None" and keeping it as loaded matrix, none_type was produced.

Thanks!

[DaneseAnna]

Thank you very much for reporting the error.
The issue should be fixed now if you install episcanpy latest Github version like such:
pip install git+https://github.com/colomemaria/epiScanpy

We uncover a subsequent error in epi.pp.load_metadata which we are solving ASAP and upate the tutorial. Once this is finalized, we will release a new version of epiScanpy and close this issue. Please let us know if you are facing any other problems.

Best,
Anna Danese

[keyingkuang]

Dear Anna,

Thank you so much for your reply. When I installed episcanpy latest github version, the function ct.build_count_mtx() still did not work (the code ran but no output files were produced).

I also have some questions regarding this function.

1. The standard input files for this function are methylpy methylation summaries for single cells and some sets of annotations. If I have .tsv files summarized using 1-based genomic coordinates and are in the following format: . What would be the best way for me to pre-process to get the count summaries?
2. For the set of annotations, are they dataset specific or where I could download those species-specific .bed files?

Thank you so much for your help!