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LOMPE annotates with VEP, uses svdb for freq - should be fairly doable!
https://github.com/kristinebilgrav/LOMPE/
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Hi,
I'm working with short-read, enzymatic converted human genome reads produced by nanopore. The expected read-lenght is about 150-200bp; + additional Illumina adaptors + nanopore adaptors; so i t…
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Olivia and I (Alyssa) will be working on the synthesis of "the 6" for our Superlab project at Haverford College this fall. We will be following the synthetic scheme outlined in #401, pictured below. …
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I recently run in to trouble setting a site instance (not a single app) in pythonanywhere, basically the problem is that in pythonanywhere they take care of the wsgi stuff so to deploy the site you ha…
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Hi @ArtRand,
The following command which I believe to have executed on identical files in the past (perhaps on 0.3.0) seem to produce the error below now:
```
modkit dmr multi \
-s methylat…
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Hi,
I am working with WGBS data and would like to use DMAP2 to investigate the differences in DMA methylation. Since I am working with a non-model organism our genome is not very polished and stil…
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There have been many changes since I last worked on this package, including:
- The [**SummarizedExperiment**](https://github.com/Bioconductor-mirror/SummarizedExperiment) package is now much more matu…
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New issue so we can keep a track of running of scripts.
I'm currently test-running the annotation pipeline on the cluster, without PhaseMatch2. I've edited the size classes based on the density plo…
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Is it possible to dump the read ids corresponding to those reads which supported a variant from `nanopolish variants`? I would like to use this for haplotype phasing.
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Currently we are migrating traditional genome analysis to Hadoop and also for learning purpose. We are using bsmap for bisulfide methylation extraction (methratio.py with input = .ba file and reerence…