David Eccles (gringer)

For showing the overall coverage, I expect this would involve adding an additional fwd/reverse feature filter: https://github.com/GMOD/jbrowse-components/blob/fc601154b770b299d966dae8a858081981c5316c/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts#L119-L132 My guess: const feats = [...features.values()] const coverage_fwd = feats.filter( f => (f.get('type')...

Here is a reference assembly and BAM file that can be used for testing (the same one that I used in the JBrowse2 picture). This BAM file is useful because...

Should look something like this: I needed to dig down to the SNPCoverageAdapter bin function to create additional scores for forward and reverse strand, in order to get this working....

I've attached a diff (based on commit 85973e53). This creates a new `StrandedRelCoverage` Display Type and associated adapters (based on `LinearSNPCoverage`), which has a stranded coverage track *and* stranded variant...

It'd be really useful to have fast5 files sorted by chromosome/position. That'd be a lot of effort to set up, though.

Sorry, missed this question. I've done a super-accuracy recall (with guppy v5.1.15 / 6.1) with my mouse cDNA reads, but not yet the nippo mtDNA reads. I'll put that on...

I've created an updated dataset, with a slightly more curated dataset that filters on the following conditions: * length >= 3kb * target (mitochondrial) match length >= 50% OR *...

Now for the accuracy comparisons. I'm checking the assembled genome using LAST (with default mapping parameters, because I expect it to be very similar to the corrected assembly), and measuring...

Revisiting those plots... canu does a *really* good job at read correction, essentially eliminating the random SNP errors, and most INDELs. The problem (as previously observed) is that it leaves...

Here's an example SAM file [attached] [mapped_BC01.sam.txt](https://github.com/arq5x/bedtools2/files/5375622/mapped_BC01.sam.txt) which should appear in the bedgraph file as a single interval. My attempted modification using the above patch produces incorrectly split output with...