Visualization on each step of the workflow

[vinadiscar]

Hi @nadiadavidson,

I'm using this documentation: https://github.com/Oshlack/Lace/wiki particularly on the given tutorial example "Differential Transcript Usage on a non model organism".

I have 2 questions:
Q1. How can I visualize results in each of the following steps: (2) Cluster contigs (e.g. with [Corset]or [RapClust] (3) Construct superTranscripts (e.g with Lace) (4) Map reads to superTranscriptome (e.g. with [STAR] (5) Count reads per exon/block feature (e.g. with [featureCounts]. Is there a sample manual of codes or scripts for visualization?

Q2. I am using an existing different transcriptome assembly not assembled from the original RNA seq reads, but from the same species. Is it possible to use this assembly for this 'SuperTrasnscript' pipeline by starting with the second step, Cluster contigs?

Thank you!