In this session we will continue annotating sequences, but now with a focus on transcripts, which can be coding and non-coding. In fact, the same gene can encode both coding and non-coding transcripts (Poliseno, Lanza, and Pandolfi 2024):
TBD including short and long reads, assembly with/wo ref, trinity, stringtie, spatial transcriptomics, expression dbs, etc
We will follow the GET_HOMOLOGUES-EST protocol at:
https://eead-csic-compbio.github.io/get_homologues/plant_pangenome/protocol.html
Your work is to run both protocols and write a brief report with:
Please make a folder named ‘transcripts/’ in the same GitHub repo of session 1, and write a report explaining i) how you solved the exercises, explaining the results, and ii) the problems you faced. See more recommendations here.