David Eccles (gringer)

I've had no further mapping problems with the new version of GraphMap; everything seems to be working fine.

As a direct comparison with gyroid, the patterns are similar, and the mass of the extruder will be moved to similar places (i.e. they're probably fairly similar in speed). Here...

Just in case it helps, I've written a script to splice out cell barcode linker sequences and shift them to before the polyA. In the process of doing this, it...

After discovering the alternative geometry format, I see that unmodified Rhapsody reads should have the following settings: --umi-geometry '1[53-60]' --bc-geometry '1[1-9,22-30,44-52]' --read-geometry '2[1-end]' There's a bit of a challenge regarding...

Rhapsody has introduced a new, shorter cell barcode specification to work with 51bp R1, which looks like this: ``` 5' PFX - CLS1 - L1 - CLS2 - L2 -...

@lh3 the linux coreutils sort command creates temporary files when the sorted structure cannot be fit into memory; it's also pretty fast. Have you considered using that, or implementing a...

If you don't want a random read to be picked for the assembly path, then it's probably not a good idea to use miniasm. Miniasm is great for scaffolding, but...

I've attached an example patch for this; thanks heaps to @cmdcolin for helping me to navigate the code. This uses the combination of reference and sequence variants to determine the...

I've been using faceted tracks for our RNASeq data as well; we've got about 160 different samples (mostly in-house, but some publicly-available data). Here's an example of our use (currently...

Looking at the 'category' key, I'd be okay using the existing JSON structure for this, with slight modifications to make it match what the documentation says: $ jbrowse add-track --help...