search

jts / nanopolish

Signal-level algorithms for MinION data
MIT License
568 stars 159 forks source link

A few questions about using nanopolish to estimate poly(A) tail length #1125

Open lopp1Y opened 9 months ago

lopp1Y commented 9 months ago

Hi,I'm running the module how to estimate poly(A) tail lengths from nanopore native RNA reads, and I've got the result file, but I don't understand the result file right now, I think this command line: nanopolish polya --threads=8 --reads=data/30xpolyA.fastq -- bam=data/30xpolyA.sorted.bam --genome=data/enolase_reference.fas > polya_results.tsv

The data in this command line is fastq, bam, fas, the explanation of this module in the literature is to use the hidden Markov model for segmentation of the raw sequencing signal , I would like to ask which of these has the information that provides signals for the hidden Markov model to analyze? What I understand is that fastq is the base sequence and BAM is the sequence alignment result. Or does this provide additional signal information? Can you help me with that? Thank you .

jts commented 9 months ago

Hi @lopp1Y,

Before running nanopolish polya you should have run nanopolish index, which builds a map from the basecalled reads (fastq) to the signal reads (fast5/pod5). This allows nanopolish to access the signal data.

Jared