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Ying-Lab / scIBD

A doublet detection tool for scCAS data
MIT License
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Is preprocessing.ipynb available? #1

Closed jeanmonet closed 9 months ago

jeanmonet commented 10 months ago

Hi,

Thank you for your work and for uploading the code.

In the file https://github.com/Ying-Lab/scIBD/blob/master/scripts/Description.txt there is mention of some preprocessing.ipynb which supposedly covers the preprocessing steps required to obtain the input to scIDB, ie the count matrix.

Is it possible to make this notebook available?

Ying-Lab commented 10 months ago

We appreciate your notice on our work and we apologize for missing the preprocessing scripts. The preprocessing pipeline mainly follows the pipenline in https://github.com/r3fang/snATAC, which demands several dependency tools, including bwa (alignment), samtools (sort), snATAC/SnapATAC (quality control & creating matrix), MACS3 (call peak) and sinto (convert BAM to fragment).

Considering that the BAM files and fragment files are the most frequently-used files after single-cell sequencing, we start with such file formats. The detailed preprocessings will be presented in a Linux shell script, while the corresponding tools may be installed at advance.