Transcriptome assembly: PacBio IsoSeq pipeline

You should be able to answer these questions if you successfully completed tutorial PacBio: the Iso Seq pipeline .

Questions

• How many transcripts are in this dataset?
• How long is the shortest isoform? And the longest?
• Can you find the ICE cluster ID? Hint
• 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?

Transcriptome assembly: MinION 2D + Canu pipeline

You should be able to answer these questions if you successfully completed tutorial MinION: error correcting 2D reads with Canu .

Questions

• What's the difference between the hybrid and denovo error correction?
• Can you explain what happens in the correction piepline of Canu? Hint.

Next

Go to next section (Tomorrow!) Assessing quality of genome assembly .

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