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COMBINE-lab / alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
https://alevin-fry.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Cannot get output #129

Closed wangjiawen2013 closed 5 months ago

wangjiawen2013 commented 5 months ago

Hello

I tried to reproduce the process according to the documentation in https://combine-lab.github.io/alevin-fry-tutorials/2023/simpleaf-piscem/

It displayed everything is fine: image

However, there is no data in the output: image

And /simpleaf/plist/10x_v3_permit.txt is an empty file.

What's wrong with it ? I nearly copied the whole code on the tutorial !

rob-p commented 5 months ago

Hi @wangjiawen2013,

Thanks for sharing your report here. I'm tagging @DongzeHE as he will be able to help as well. I can see that you're using simpleaf to run alevin-fry and to do the mapping etc. Can show the result of doing ls -la pbmc1k_quant/af_map?

I suspect the issue may be related to the 10x_v3_permit.txt being empty — that's certainly not right. Since it's hosted on "Box", that link sometimes misbehaves, we will check it. In the mean time, can you try downloading the 10x_v3_permit list from this url https://umd.box.com/shared/static/vc9zd4qyjj581gvtolw5kj638wmg4f3s.txt and placing it where it should reside?

--Rob

wangjiawen2013 commented 5 months ago

It worked with the new permit list