Kim IVT Cov Track Settings
 
Kim 2020 in-vitro-transcribed RNA seq + PCR: Nanopore coverage   (All Mapping and Sequencing tracks)

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Data last updated: 2020-06-11 06:11:30

Description

This track shows the coverage of Nanopore sequences from Kim et al. 2020 obtained after in-vitro reverse transcription and tiling PCR of SARS-CoV-2 genomes. This is not direct RNA sequencing, but multiplex PCR on DNA, followed by sequencing. The coverage shown here does not allow to draw conclusions on RNA modifications or RNA editing, but indicates regions of the genome that are harder to sequence with Nanopore sequencing.

Display Conventions and Configuration

Sequence coverage of every bp is shown. All reads were used.

Related tracks

  • ARTIC primers: a set of well-known primers used for PCR + Nanopore sequencing.
  • Kim Transcripts: transcripts as determined with direct RNA sequencing by Kim et al. 2020
  • Kim RNA Brkpts: locations where RNA tends to break, as determined by direct sequencing by Kim et al. 2020
  • Kim RNA Modif: modified bases in the direct RNA sequencing relative to the IVT sequences.

Methods

Minimap2 alignments BAM files were processed with bamCoverage.

References

Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H. The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020 May 14;181(4):914-921.e10. PMID: 32330414; PMC: PMC7179501