Welcome to NanoCount v1.0.0.post6 documentation
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
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
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, https://doi.org/10.1093/nar/gkab1129
Copyright © 2020 Adrien Leger
The package was inspired from https://github.com/jts/nanopore-rna-analysis by Jared Simpson
- Jared Simpson (@jts)