error occured whe running Epinano_Variants.py

[Seongmin-Jang-1165]

hello

i ran Epinano for analyze m6a modification with oure Direct RNA seq data

but when i started, it did not work and the error message is below:

Please offer correctly path to sam2tsv.jar

how can i fix this error?

i ran Epinano under Bioconda Environment

[enovoa]

Please check the version of Epinano you are using, as stated in the README and the description of Epinano_variants.py, Epinano v1.2.4 does not rely on sam2tsv.jar any more

[Seongmin-Jang-1165]

@enovoa
thanks for advice!

does basecalled data for Epinano must be generated using Guppy3.1.5? my data is POD5 format and i tried to run Epinano with DORADO basecaller

[enovoa]

Hi @Seongmin-Jang-1165, sorry for late reply. Epinano-SVM can only run on data basecalled with Guppy 3.1.5. For EpiNano-Error, you can use data basecalled with dorado. However, I should note that its performance with RNA004 data and recommended settings have not yet been fully benchmarked, we are in the process of doing this for different RNA modification types. Thanks!

[enovoa]

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