Hi, Am trying to process some sequencing data from ONT. I have fast5, fastq, fasta files. I have also generated bam files with minimap2 and samtools. However, when I cam trying to run Nanopolish, ELIGOS2, DRUMMER, Tombo - all tools are giving me errors. I cannot process my reads. My guess is that some plugin needs to be installed and CONFIGURED CORRECTLY to make the programs read the fast5 current signals along with the reference genome and bam files. Can anyone help me out ? I am doing ONT data processing for the first time and it is a bit urgent. Thanks! :)
This is the error from tombo resquiggle command :
This is the error sample from nanopolish call methylation command :
My goal is to analyse RNA base modifications from direct RNA sequencing using ONT. I am doing it for the first time and trying multiple tools for the same, with no success in any yet. I have fast5 files, base called fastq files as well. I need to analyse the current change patterns to detect the methylation pattern changes in treated and control samples. Any guidance on this will be really helpful. Thanks :)
Hey, Am trying megalodon now for rna methylation analysis. Could you help me out with this error?
I think you're misspecifying the configs. Also, I would combine the reference genome/contigs into one file and specify that directly. Megalodon seems to like full paths. Heres' what I use for dna from promethion (nextflow code, variables are full paths, using GPU as needed for Megalodon).
Also I would ask the ONT devs via the Megalodon github repo what current best practices are for rna, think it's v tricky.
This list might help get you started too https://github.com/GoekeLab/awesome-nanopore
Thanks! I tried tombo and am still doing with no success.
Which config file to use? My guess is megalodon shows the error due to this reason only!
Hello, Could you solve your problem? I am having the same problem over here.