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Hello,
I am trying to run this for a set of raw sequences for Anopheles gambiae. I used EDTA to create a TE library from the agamP4 genome assembly and then used my raw sequences as input for this …
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@DomNelson and I were just discussing the possibility of adding support for multiple chromosomes to tskit. One possibility which seems like it might be a reasonably smooth path forward is the followin…
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I am new to wfmash (but of course have plenty of alignment experience).
I tried an experiment in which I generated a random genome and a second with rearrangements (including random reversals) of i…
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_WARNING: long post below. I'm hoping to help us build a shared conceptual framework to guide ongoing API design, and given the underlying complexity and the number of different priors, don't know how…
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In a test sample I'm finding that `selectSolution` is not selecting "what should biologically speaking" be the best solution.
For some reason, it prefers this ploidy=4, clusters=3 solution:
…
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Jeremiah;
Now that we have VariantBam maximum coverage downsampling in bcbio (thank you again), we've been working on doing benchmarking runs with and without downsampling. Because we need to run it …
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Thoughts, implementations and advice welcome!
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From email:
Looking at the model data, it would be something like this:
{reactions: Array[1051], compounds: Array[1103], genes: Array[1956], compartments: Array[2], biomass: Array[100]}
Where each…
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Running woltka classify as "Step 2: stratified functional profiling" with preserved --outmap in first woltka classify for taxonomy and got this error:
cat ~/plasma_woltka_strat-1.e1315562
Tracebac…
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We talked about this already, but I'd like to take action and update the Datastore where appropriate.
There are a number of `gene_models_main` GFFs that have the **Name** attribute starting with _g…