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adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
https://www.cbu.uib.no/valen/
GNU General Public License v3.0
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Cols Function #52

Open Mighty-chondrias opened 1 year ago

Mighty-chondrias commented 1 year ago

I am trying to use the R package to analyze nanopore RNA-seq data. I am inserting basecalled fast5 files. The package recognizes the files, processes them, creates a csv but all the columns are empty and it says you need to use the cols function. I cannot find any documentation as to how to use the cols function. Furthermore since the fast5 files are binary I do not even know how you would define columns from that.

adnaniazi commented 1 year ago

Hi,

Thank you for trying out tailfindr.

It seems like the VBZ plugin is not installed correctly.

Please extract the tar file of VBZ plugin and then do like this (on Linux):

export HDF5_PLUGIN_PATH=/bla/bla/bla_path/vbz/ont-vbz-hdf-plugin-1.0.1-Linux/usr/local/hdf5/lib/plugin

Try running tailfndr again on a subset of your reads to test. Hopefully, it would work.