nanopolish
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jts
Signal-level algorithms for MinION data
Hi @jts Is it possible to "nanopolish polya" with guppy 6.0.6 called fastq files? Or do only albacore basecalled fastq files work with the command? Seen from the documentation, it...
I wonder if the use of Nanopolish after a canu assembly processed on duplex reads is still of interest in your opinion? If yes, is it possible ? Thanks Jared...
Dear, I would like to use nanopolish to call methylation for 5mC, 6mA, and 4mC. When I try it using following commands, it works and seems to produce a normal...
Hello, I want to share a problem that I am unsure how to solve. Initially, I have effectively installed the Nanopolish onto the cluster that is currently under my purview,...
Hi there, thanks for developing nanopolish for ONT data analysis! I am working on the direct RNA sequencing data and would like to use nanopolish to align the events. I...
Hi, I would like to know if the command _nanopolish eventalign_ changes the file size/content of the sequencing_summary file we specify in the command. If so, why? Since we are...
Hello, I have two samples of 30x ONT data without any repeats or WGBS testing. My goal is to compare the differential methylation level between these two samples(for instance, in...
Hi, I tried to install as recommended: ``` git clone --recursive `https://github.com/jts/nanopolish.git` cd nanopolish make ``` and I obtained many warnings. Example: ``` file_image.c:27:58: note: in expansion of macro ‘FAIL_PUTS_Endition))...
Hello, I’m working on running nanopolish for methylation calling. My command line was: `nanopolish call-methylation -t 8 -r /home/choilab_tk/nanopore/data/221108_bank7492_NIID_Cas9/20221108_0927_X5_FAV43835_7491c0d0/fastq_pass/pass/merged/output_merged.fastq -b /home/choilab_tk/nanopore/results/221108_bank7492/minimap2/merged/output_merged.bam -g /home/choilab_tk/hg38/hg38.fa -w "chr1:149,390,100-149,391,900" > methylation_calls.tsv` However, when I...
Hi, I know Nanopolish can output both tsv and modified bam when calling methylation but I wondered if you had (or knew of any) available scripts that would convert modified...
