4_nanopore_sequencing_extended.html

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layout: slides
title: "Further Imformation about Nanopore-Sequencing"
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### Technical Remarks


- Double strands are required for nanopore-sequencing, because single strands would stop at the point where you have your adapter (ds position).
- The nanopore itself is strong enough to open up the ds. A helicase is not necessary.
- The MinION has 4 pores for 512 channels (in total 2048 pores).
- During the sequencing the MinION uses only one pore per channel. Every hour the lane will be checked and perhaps the MinION swaps to a different pore.
- The quality of the reads decreases at the end of a read like in Illumina Sequencing.
- Average length 2-10 kb reads. Error Rate 15-40%.
- Change between template and complement strand is recognized by a specific signal of a site located in the hairpin adapter.
- [Literature](https://www.researchgate.net/publication/317848322_Nanopore_sequencing_data_analysis_state_of_the_art_applications_and_challenges)

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### Base Calling


- Decoding the raw current signal into a base.
- Long stretches of the same base might induce a higher error (e.g., Poly-A-Tail problem).

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### RNA Sequencing


- RNA sequencing is possible but so far you need to do a RNA PCR into ds strands (see technical remarks).
- Also possible is the standard way of a reverse trascription into cDNA and then a cDNA PCR.

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### Max Scan


- It is the name for Nanopore's Current Checking.
- It will automatically determine which pores has the best electric field.
- Then the MinION will pick those pores for seqeuncing.
- This feature is important, since the quality can change over time for the base calling of the each pore.