Welcome to NanoCount v0.4.0.post4 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 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
The repository is archived at Zenodo. If you use NanoCount please cite as follow:
Adrien Leger. (2020, January 28). a-slide/NanoCount. Zenodo. https://zenodo.org/badge/latestdoi/142873004
Copyright © 2020 Adrien Leger
The package was inspired from https://github.com/jts/nanopore-rna-analysis by Jared Simpson
- Jared Simpson (@jts)