Hello,
I am trying to call modified bases from the Direct RNA Sequencing Kit (SQK-RNA002) with the R9.4.1 Flow Cell and the MinION Mk1b. When I print workflows there are no config files available with my kit, flow cell, and that have modbases written in the name. Why is this? is there one available to download? or will i have to use another tool?
The exact folder structure may be different based on your installation or version, but if you look in a folder like /opt/ont-guppy_x.y.z/data/ or /opt/guppy_x.y.z/data/ you will find model files that are missing from the --print-worklows output. I don't know why though :-)
So, I know there is a basecalling config available for my kit called rna_r9.4.1_70bps_hac.cfg. However, I have seen configs named to include modified bases. For example, in the ont-guppy-x.y.x/data folder there is a file named dna_r9.4.1_450bps_modbases_5mc_cg_hac_prom.cfg. I'm wondering why there isn't one available for rna_r9.4.1? The kit I used mentions it can be used for modified base calling so I thought that ONT would have a config named like 'rna_9.4.1_70bps_modbases_5mc_hac.cfg'. However, this is not the case (even in --print-workflows). As I mentioned above, I found that the modified bases information can be extracted from the BAM file. Is this what we are expected to use? If so, how does it differ from using a "_modbases_5mc_cg" config?
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version 2.3.6
are you sure this is a model released by ONT?
Yeah, the MinION [Mk1b] just doesn't have the live basecalling and screen and like the newer MinION Mk1c. I got the fast5 from the initial run. However, I am using the command line guppy_basecaller from the software downloads page of nanopore community. The kit I used says it can be used for modified bases online so I assumed they would have a config through guppy.
i am not certain, but I would probably check with ONT technical reps first. sorry to not be of more help.
Looks like you can still detect modified bases in the BAM file Nanopore: Can I detect modified bases? and the recommend tool to visualize modified bases is pycoMeth pycoMeth github.
That is not what OP is asking for.