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Welcome to NanoCount v1.0.0.post6 documentation


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NanoCount estimates transcripts abundance from Oxford Nanopore direct-RNA sequencing datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads

Quick start

Align reads

Reads should be aligned to a transcriptome reference using minimap2. We recommend using the -N 10 option to retain at least 10 secondary mappings.

minimap2 -t 4 -ax map-ont -p 0 -N 10 transcriptome.fa.gz reads.fastq.gz | samtools view -bh > aligned_reads.bam

Estimate transcripts abundance with NanoCount

NanoCount -i aligned_reads.bam -o transcript_counts.tsv

Detailed instructions


The repository is archived at Zenodo. If you use NanoCount please cite as follow:

Josie Gleeson, Adrien Leger, Yair D J Prawer, Tracy A Lane, Paul J Harrison, Wilfried Haerty, Michael B Clark, Accurate expression quantification from nanopore direct RNA sequencing with NanoCount, Nucleic Acids Research, 2021;, gkab1129,



Copyright © 2020 Adrien Leger


The package was inspired from by Jared Simpson

  • Jared Simpson (@jts)