Looking to use SAMap to analyze datasets from mouse and zebrafish single cell.

atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

MIT License

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Looking to use SAMap to analyze datasets from mouse and zebrafish single cell. #82

Closed otoky closed 2 years ago

otoky commented 2 years ago

I am having trouble understanding how to run the reciprocal BLAST and generating the two tables i need. The tutorial isn't helping and wondering if there are any resources for me to get this to work!

Thanks

atarashansky commented 2 years ago

Hi, @otoky

Can you download the jupyter notebook and open it locally? The first few cells should give you what you need. They don't render in github for some reason :(

If you have already seen those instructions and are still having trouble, please let me know where you're getting stuck and I'll help you get the ball rolling.

otoky commented 2 years ago

Thanks! Working through the downloaded tutorials now! This is a really awesome way to cross species analysis so I'm excited to get this to work

otoky commented 2 years ago

I am having trouble getting the jupyter notebook to run from the run_image.sh- when i open the referenced port, it says access denied

atarashansky commented 2 years ago

Docker support is deprecated for now as it requires significant overhaul to be less flakey on other machines.