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What genome reference was used? How was it processed for CellRanger? #5

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ChristophH opened this issue Nov 7, 2024 · 0 comments

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@ChristophH
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Hi,

Congrats to the team for having the final version of the Zebrahub paper out! It's very impressive work and a great resource.

I couldn't figure out what genome reference was used and how exactly the reference for CellRanger was built. It seems like that information is
neither in this repo, the protocols section of the project, nor the method section of the paper.

All I found was:

To align the reads to the reference genome, a reference genome was first created using CellRanger v.4.0.0. Subsequently, the CellRanger v.5.0.1 software was used for read alignment to the reference zebrafish genome.

Could you please share the commands that you used to download the reference and its annotation, and to create the CellRanger compatible reference?

Thanks,
Christoph

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