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Build kb-python reference for GENCODE release M26 GRCm39

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FFloWuenne
Last edited Feb 25, 2021
Created on Feb 25, 2021

This visualization demonstrates the command-line workflow for building a kallisto\|bustools reference index for the GENCODE mouse annotation release M26, specifically for the GRCm39 genome assembly. It shows the sequence of shell commands required to set up a Python virtual environment, install the kb-python package via pip, download the primary assembly genome FASTA and annotation GTF files from the EBI FTP server, and then run `kb ref` to generate the index, transcript-to-gene mapping, and cDNA files. The code relies on the `kb-python` API and standard Unix tools like `wget` and `module load`, with the process occurring on a compute cluster.

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