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i am doing nanopolish-eventalign for my nanopore direct RNA sequence reads.
I have 9 samples, for a sample the command is running for more than 24 hours and is not able to complete within time limits…
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Hi,
i have done the partitions of the fastq file as it was not finishing for whole fastq in time.
so now i have eventalign.txt file for each part. I am using m6anet for pred the m6a sites.
wha…
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Hi,
I got pod5 files and fastq file, and want to call methylation. I know Nanopolish does not support pod5 files, so I used blue-crab to convert pod5 files to blow5 files. Then I used slow5tools to …
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Hello everyone,
New user here. I have been trying to run artic pipeline here.
Right after align_trim, I get lines and lines of error message and assembly finishes. Even though I have viral assem…
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generate bam with minimap file that it's going to be used by nanopolish.
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Hi,
I got the following error when I ran nanopolish eventalign. There isn't any other error message. I have run nanopolish eventalign with my other samples and it was fine.
**/var/spool/slurm/d…
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Hi Shian,
Thank you for the program!
I might be asking a silly question. I am currently using modkit, but I don't find a way to obtain a table that resembles your "methy" object in the user's g…
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Hi,
While trying to run the Nanopolish snakemake with the example data I get the following error:
RuleException:
WorkflowError in line 25 of /METEORE/Nanopolish:
HTTPError: HTTP Error 404: No…
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Hi there,
I am wondering if applying Nanopolish makes sense after an assembly with ONT data that were basecalled by Bonito.
When I look into the Nanopolished assembly, I found some errors were newly…
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Dear Shian,
I was working with with tsv files output from Nanopolish and tried inputting them in NanoMethViz.
Nanopolish is capable of producing methylation for 5mC, 6mA, and 4mC patterns.
Lo…