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Welcome to NanoCount v0.4.0.post4 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 must be aligned a transcriptome reference using minimap2 with -p 0 -N 10 options to retain up to 10 secondary mappings without filtering. NanoCount will take care of the low score alignments internally.

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:

Adrien Leger. (2020, January 28). a-slide/NanoCount. Zenodo.



Copyright © 2020 Adrien Leger


The package was inspired from by Jared Simpson

  • Jared Simpson (@jts)