callumparr

Hey I was look to repurpose your read_length.py script and also wanted to use R script. I was wondering how did you generate the read_data.tsv file, is this coming from...

Clear memory from complexUpset plotting without having to restart Rsession

2

**Objective** Is there a way to clear the objects stored in R memory after running complexUpset? Currently creating an upSet plot with additional attribute plotting that fills up most of...

Is it possible to customize the y-axes limits when using boxplot.summary. I have an attribute that is the read length of some nanopore sequencing where most data lay within 100...

Expect epoch time for training

2

I am running `bonito train test` on a node that has 2 x T4 Tesla, I tried running with --multi-gpu but it would run out of memory even when reducing...

I run following command and submitted to cluster using `qsub` on a `bigmem.q`: ``` #!/bin/bash # Set source of conda install source miniconda3/etc/profile.d/conda.sh conda activate xpore export baseDir=/analysisdata/rawseq/bcl/callum xpore-diffmod --config...

No error model errors when using --ont option

10

Version 1.5.2 downloaded binary for linux system from GitHub. Judging but the length of the log output I do not think this applies to all alignments but certainly some alignments...

I recently ran quite a few DRS libraries and want run poly-a analysis using nanopolish. I'd say its only worth running on PASS reads. However, I am running into the...

Scripts to extract mod info from hdf5 files

2

Is there any scripts or example code to extract mod probabilities outputted to hdf5 by the basecaller.py script using h5py. I do not have any experience with python code and...

Is the output DTU transcript.tsv file the p.values or adjusted p.values? Is there a standard threshold to apply for statistically significant DTU entries?

https://github.com/COMBINE-lab/salmon/issues/602#issuecomment-748729130 Having read this I was wondering if I should be using the --noLengthCorrection that mean the TPM will be more meaningful for Nanopore reads and perhaps the NumReads, although...