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colomemaria / epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

BSD 3-Clause "New" or "Revised" License

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multimodality #31

Open wangjiawen2013 opened 4 years ago

wangjiawen2013 commented 4 years ago

Glad to be the first one here! Looking forward to the final release version of epiScanpy and it's full tutorial and the download link of test data. By the way, Could epiScanpy be used as a multi-modal analysis tool as discussed in https://github.com/theislab/scanpy/issues/479 ?

wangjiawen2013 commented 4 years ago

I am following the tutorial now, when I run: epi.ct.bld_atac_mtx(list_bam_files=list_cells, loaded_feat=enhancers, output_file='test_ATAC_mtx.txt', path=path_to_play_data, writing_option='w', header=enhancer_names)

an error occurs: pysam/libcalignmentfile.pyx in pysam.libcalignmentfile.IteratorRowAll.next() OSError: truncated file perhaps it is caused by samtools or pysam's version

Besides, the default value of parameter "chromosome" of function epi.ct.bld_atac_mtx is mouse genome, while that value is human genome in function epi.ct.load_features() is human. Why don't keep them the same ?

wangjiawen2013 commented 4 years ago

And the title of epiScanpy homepage is wrong, it should be epiScanpy, not eoiScanpy ! https://episcanpy.readthedocs.io/en/latest/

DaneseAnna commented 4 years ago

Sorry, for the delayed answer.

We have been working into making episcanpy a true multi-modal analysis tool. This is not fully implemented yet but I will post an update regarding this point soon.
Due to compatibility problems as well as other issues encountered with pysam, we switched to bamnostic in a later version of episcanpy.
We arel making sure to put the same default value of parameter "chromosome" in the later version of episcanpy
Episcanpy homepage have been updated to remove typos. Thanks, I was completely oblivious of this huge typo.

Thank you for all your remarks, this is very helpful!