This is a repository of scripts that were used in the paper "Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex" by SK.Leung, A.R.Jeffries,..E.Hannon,J.Mill.

Raw PacBio Iso-Seq data have been deposited in the Sequence Read Archive (SRA) database under accession numbers PRJNA664117 (human cortex) and PRJNA663877 (mouse cortex).

UCSC genome browser tracks of our processed Iso-Seq data (filtered and unfiltered) together with a visual database of cortical isoforms are available at: http://genome.exeter.ac.uk/BrainIsoforms.html.

Intermediate files (gtf, fasta) generated from Cupcake and SQANTI2 (v7.4) can be downloaded through Zenodo (DOI:10.5281/zenodo.7611814)

The scripts are categorised under:

1. Processing Iso-Seq data: Iso-Seq3.1.2 Pipeline and Post-Iso-Seq pipeline
2. Comparisons with RNA-Seq at gene and isoform level
3. Novel Genes
4. Characterisation of Alternative splicing events
5. Differential Transcript Usage
6. ONT analysis
7. Disease
8. Output - Figures, Tables, Rmarkdowns
9. Web Resources

See Wiki for more details!