Introduction

Section: Transcriptome assessment [1/4].

Now that you have your transcriptome from PacBio and MinION, we can go check the actual content of these files and get an overview of what are the transcripts that we have assembled. For this, we propose two methods here: (1) aligning the assemblies to the reference genome in splice-aware mode and (2) compare these alignments to the reference transcriptome.

As for genome assembly, there are some metrics allowing to assess the quality of your transcriptome, but we're not going in the details here today. As for genome assembly, these metrics can be partitioned into two categories: (1) continuity metrics (e.g., the E90N50 transcript contig length, aka the contig N50 value based on the set of transcripts representing 90% of the expression data) and (2) completeness metrics (e.g., BUSCO to explore completeness according to conserved ortholog content).

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