callumparr

> I now need to wait again to get a valid MPD to test with, unfortunately they seem to move the replays to the older system that works just fine,...

I've tried gc() but doesn't seem to clear anything that large. Also tried saving the plot to an object so I can rm(plot) but also still large amounts of memory...

> hi @iiSeymour ...do you by any chance have a guppy/rerio (compatible) model for the newest bonito model ([email protected])? Would also like this. I am about to embark on recalling...

somewhat related. I ran some data set through guppy 4.4.1 (I think) with either flipflop HAC or using rerio directory for bonito crf32. There seem to be some disagreement in...

> Hi Callum, I noticed that you have the same CUDA/driver versions as I have. You also appear to be using a Conda environment. I’m having trouble getting my installation...

Id be also interested in any documentation of using bonito train. Is it similar process to taiyaki? From what I understood from the Nanopore Community meeting when Clive gave a...

I had to create env using `python=3.8` for pip to install 0.5.6. Would it be OK to update the readme for installation? Also it be useful for others to include...

I do not know but it would not run if I did not generate eventalign with that during the nanopolish dataprep would not run. https://github.com/GoekeLab/xpore/issues/37 this issue seems to state...

I am also getting same error when using the test data set. Is there a solution for this. ``` bonito train test --multi-gpu --directory /home/callum/miniconda3/envs/bonito/lib/python3.8/site-packages/bonito/models/dna_r9.4.1 ``` ``` [loading data] [loading...

map-ont isn't specifically for DNA per se it is for overlaps when you don't need to account for gaps. Aligning mature RNA (polyadenylated) to transcriptome comes under this category of...