callumparr

I have used "U" as was default in config.yml for pipeline-transcriptome-de but now I am thinking it should be stranded but i am not understanding the reverse part? Should it...

loss in mapped squiggle for RNA reads is also compounded by polyA absent from guppy called fastq. > supplementary question： > Does the decline of the loss curve indicate that...

OK it seems my issue with NanoComp is stemming from the NanoPlotter / NanoPlot. It be great to export static plots for presentations. It's a bit of a faff to...

For cDNA, you may use this tool primer-chop. It does a similar thing to pychopper for stranded libraries in addition to also trimming the polyA tails. You can add your...

> Your intuition that internal priming / the reproducibility filter should not be affecting these numbers is correct. > > I'm looking into it otherwise. I've checked a log file...

I looked into it a bit more and I am still at a loss why some reads are failing. This was consistent across multiple samples although all processed the same...

config tells pychopper in what orientiation to expect your adapter/primer sequences used to make the full-length cDNA library. So for instance it be odd to have a read that both...

This was actually an older version from 2019 but I rerun with 4.4.1 and the qualities seem similar. Just looking at accuracies now. I did see that bonito consistently gives...

Also interested to know. When this happened I just deleted the database and initialize a new one as there isn’t a —resume flag.

> What I typically do is I make a backup copy of my TALON database before trying to add new datasets to it. That way, if the run fails, I...