search

colomemaria / epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python
BSD 3-Clause "New" or "Revised" License
139 stars 33 forks source link

Help needed in preprocessing scATAC-seq #68

Open alirezaomidi opened 3 years ago

alirezaomidi commented 3 years ago

Hi,

I want to preprocess some scATAC-seq datasets properly. I have seen episcanpy tutorials. I do binarization, variant peak selection and use regress_out method but still get poor results. Would you suggest me what to do in order to get better results? I have uploaded two of my preprocessing notebooks here and here.

@DaneseAnna

DaneseAnna commented 3 years ago

Hi, Thank you for your feed back. You should avoid regress_out for now. Try increasing your number of features to 40k and use epi.pp.normalize_per_cell to correct for library size. I hope it will help you.