Colab_instruction.md

Instructions for using the Colab notebook to predcit transcriptome

1. connect to a GPU instance

click the triangle on the top right corner and select Change runtime type

Then select T4 instance and click save

After connecting to a T4 instance, you will see this on the top right corner:

2. upload genome sequence and annotation files

click the files button on the left:

Then click the upload to session storage button:

Select genome sequence and annotation files from the local folders, please note that two files should have the same name: e.g., GCF_000011065.1.fna and GCF_000011065.1.gff

3. running the codes

Please click the run button for three parts of the codes, including Install, Generate embeddings and Predict gene expression:

The predicted gene expression will be automatically downloaded as a csv file.