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Cellular Genetics Informatics Notebooks
https://jupyter.cellgeni.sanger.ac.uk
GNU General Public License v3.0
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Different genome references #2

Open ilyakorsunsky opened 5 years ago

ilyakorsunsky commented 5 years ago

Thanks for this very timely resource! It looks like in the benchmarks of 10X pbmcs, one of the datasets was quantified with hg19 but the others with GRCh38. Is this intentional to integrate across different references? In a similar benchmark in the Harmony paper, I remapped everything to GRCh38. Not surprisingly, it made integration much easier

wikiselev commented 5 years ago

Interesting, thanks for the insight! We have not looked into that yet, for ease, just downloaded the datasets from the 10X website.