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105729b Jan 18, 2018
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Direct RNA and cDNA Sequencing of a human transcriptome on Oxford Nanopore MinION and GridION

Introduction

We have sequenced the CEPH1463 (NA12878/GM12878, Ceph/Utah pedigree) human genome reference standard on the Oxford Nanopore MinION using direct RNA sequencing kits (30 flowcells) and using the 1D ligation kit (SQK-LSK108) on R9.4 flowcells using R9.4 chemistry (FLO-MIN106). RNA from the GM12878 human cell line (Ceph/Utah pedigree) was extracted from the cultured cell line.

Contributors

  • Winston Timp, Rachael Workman, Timothy Gilpatrick (Johns Hopkins)
  • Jared Simpson, Phil Zuzarte, Paul Tang (OICR)
  • Terry Snutch, John Tyson (UBC)
  • Mark Akeson, Hugh Olsen, Benedict Paten, Angela Brooks, Miten Jain (UCSC)
  • Nick Loman, Josh Quick, Andrew Beggs, Jaqueline Goes de Jesus (University of Birmingham)
  • Matt Loose, Nadine Holmes, Matthew Carlile (University of Nottingham)

Acknowledgements

We are most grateful to Daniel Garalde, Daniel Jachimowicz, Andy Heron, Rosemary Dokos at Oxford Nanopore Technologies for technical and logistical assistance.

Analysis

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Basecalls (Albacore 2.1)

Direct RNA (full dataset, 30 runs)

  • Pass, 10302647 reads, mean 1030.24, N50 1334
  • Fail, 2686736 reads, mean 430.96, N50 840

cDNA 1D (full dataset, 12 runs)

  • Pass, 15152101 reads, mean 932.86, N50 1072
  • Fail, 9129338 reads, mean 661.90, N50 841

Combined Albacore Summary

Raw Signal Data

Direct RNA

All runs MinION unless noted.

Alignment Files

All alignments performed using minimap2.

Direct RNA

pass

fail

Reference Files

GRC38 and BWA indices

SIRVome

cDNA

Run by run links

External Links

Heng Li has make a custom track for the UCSC genome browser from the direct RNA dataset. Thanks Heng! [1]

References

[1] Li, H Twitter link