Mouse reference genome

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1

What is the mouse mm10 equivalent for these lines of code where you specify the transcript information for the reference genome?

gtf = pd.read_feather(

'https://storage.googleapis.com/alphagenome/reference/gencode/'

‘hg38/gencode.v46.annotation.gtf.gz.feather’

)

2

Hello @Seren_Ford, welcome to the community!

The mouse gtf is available from https://storage.googleapis.com/alphagenome/reference/gencode/mm10/gencode.vM23.annotation.gtf.gz.feather

So the following should work:

import pandas as pd


df = pd.read_feather(
    'https://storage.googleapis.com/alphagenome/reference/gencode/mm10/'
    'gencode.vM23.annotation.gtf.gz.feather'
)

Hope that helps!

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3

Dear tward,

Thank you for sharing the gtf feather file for us. Could you also share the pas, splice site starts and splice site end feather files for us, please ?

4

So the splice site starts/ends are located here: https://storage.googleapis.com/alphagenome/reference/gencode/mm10/gencode.vM23.splice_sites_starts.feather and https://storage.googleapis.com/alphagenome/reference/gencode/mm10/gencode.vM23.splice_sites_ends.feather.

We have not processed mouse polyA sites, so don’t have a feather file for that.

5

NB: The scripts used to process GTF and splice sites is available at alphagenome/scripts/process_gtf.py at main · google-deepmind/alphagenome · GitHub

6

Thank you, Tward, for providing us with the data and code!

1 Like