Checkpoint: Long Reads Transcriptome

Section: Long-reads Transcriptome [4/4].

PacBio IsoSeq pipeline

• How many transcripts are in this dataset?
• How long is the shortest isoform? And the longest?
• Can you find the ICE cluster ID?
• Why do we need to do size fractionation to get the best of transcriptome assembled by PacBio?
• Why we say that the Iso Seq pipeline is not a real assembly?

MinION 2D

• What's the difference between the hybrid and denovo error correction?
• in which cases would you NOT correct your RNA reads?
• Can you explain what happens in the correction piepline of Canu? Hint.

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