DaRinker
DaRinker
Interesting. It's not symlinked as far as I am able to determine.
The genes are all from extremely closely related "species" (branch lengths
Ah! Okay, that makes me feel much better. Thank you
No. I decided it was the wrong tool for the job. Maybe there have been developments since? Right now I'm most confident when using Kaiju on Illumina reads.
In looking at my output scaffolds in more detail, I don't think they're all correct. Not sure why, but for one reference chromosome, ragout is consistently inserting lots of small...
>In general, Ragout won't make a connection (e.g. chr1 - chr6 fusion) unless there is evidence of it in at least one of the reference genomes or the target genome....
Thanks for your input. The problem with the simplest strategy it that using only the T2T genome for each strain results in a very mixed bag of results. Some of...
I may have figured out what is going on here. These discrepancies appear to be instances of overlapping genes in the gff (opposite strands) where TPMcalculator can't assign one transcript...
I have now duplicated this error with another ONT bam-to-fastq file (again using dorado's --emit-fastq option) Visually, I don't see anything obviously strange about the fastq: > $ head barcode02.bam_trimmed.fastq...
UPDATE: Still stuck. Everything about the input fastq input seems okay (I'm able to trim it with `chopper`, quality check it with `NanoPlot`, and assemble it with `raven`). But flye...