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Annotation Database
No due date Last updated over 6 years agoAfter some discussion, Ali and I determined that the GTF reading sh…
After some discussion, Ali and I determined that the GTF reading should be handled outside of TALON itself to allow the annotation to behave sort of like a genome index. The GENCODE annotation gets read in once to create the database, and then TALON runs can add novel transcripts to the annotation base. This simplifies the issue of comparing different samples. It would no longer be necessary to allow the user to input several sam files at once. However, it gives rise to other issues. For instance, we may need to provide quality metrics to keep track of which novel events we trust.
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TALON: Exon-based comparison setup
No due date Last updated over 6 years agoImplement classes and functions needed to support a basic TALON pro…
Implement classes and functions needed to support a basic TALON prototype that compares transcripts on the basis of their exons. This prototype should be able to compare SAM transcripts to the annotated genes/transcripts to determine whether they are known or not, but also tell us about 3' and 5' differences. For novel transcripts, we should be able to tell if the novel event is a new combination of known exons, or something else altogether.