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Hi,
I am analyzing m6A call from nanopore direct RNA sequenceing data. After basecalling, the direct RNA reads contain U instead of T. I wonder if it is necessary to conver U to T in fastq file in …
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Weekly progress update of my project
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Hello,
I managed to run through the example provided so I know the code is working. But when I used a bit of sample data I generated a while back it gave me this error when I tried to index the dat…
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Hello,
I am trying to run the ARTIC pipeline on the Singularity profile with the new ARTIC V4 primer scheme set (https://github.com/artic-network/primer-schemes).
I am running the Nextflow pipeli…
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Hi @jts,
I am currently running `nanopolish index` on two direct RNA libraries, one obtained from a MinION and the other from a PromethION. The former seems to have worked perfectly fine when inclu…
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I ran the example in https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html.
However, I noticed that some reported coordinates were not pointed to C/G base and probably shift -1…
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Dear Jared,
For one variant Nanopolish is calling a Hom position as het. Below the INFO
`155205331 | . | T | C | 1794 | PASS | BaseCalledReadsWithVariant=188;BaseCalledFraction=0.817391;Total…
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Hi, sorry to bother you again
Software like Nanopolish, Tombo, and Guppy often utilize a threshold when detecting DNA methylation modifications （5mC), for example:
**Tombo**: use the recommended …
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Hello,
I am using my own scheme of primers, the directory looks like:
fieldbioinformatics/schemes
fieldbioinformatics/schemes/vc07
fieldbioinformatics/schemes/vc07/vc07.insert.bed
fieldbioinfor…
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Newer versions of MinKNOW now compress fast5 files with VBZ compression which causes `strique.py count` to fail.
Nanopore have provided an updated hd5 plugin to handle VBZ, however I'm struggling t…