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The issue discussed in #1075 highlighted that representing pseudogenes is a little tricky
Especially with a track that has both genes and pseudogenes, it would be good to dispatch to the Gene glyph…
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I am using the fasta file from here
https://www.ebi.ac.uk/reference_proteomes
because I *think* this is the dataset that GO uses.
- [ ] Question 1 IS THIS CORRECT?
I downloaded the human fi…
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[R Markdown file](https://github.com/fish546-2018/yaamini-virginica/blob/master/analyses/2018-12-02-Gene-Enrichment-Analysis/2019-01-15-Proportion-Test.Rmd)
I characterized genomic locations for al…
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Dear Dr. Vivian:
In your [Method](https://github.com/BD2KGenomics/toil-rnaseq/wiki/Methods) introduction, you mentioned Kallisto index was made using following command:
```
sudo docker run -v …
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Hi I'm thinking about using NOVOPlasty to assemble chloroplast and mitochondrial genomes from a flowering plant species (WGS Illumina data; reference from the same species available to seed the progra…
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Hi,
I have pseudogene, pseudogenic_exon and pseudogenic_transcript features in some gff files - any way to represent these on one track in JBrowse/Apollo, using flatfile-to-json.pl?
Thanks.
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Hey @vladsaveliev -- since you changed "NA" to `None` for transcript support levels, do you think we should have the value always be `int` or `None?
Also, to help me remember, pasting the meanings …
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There are 29 pseudogenes discovered in the HMR2 model based on the Ensembl annotation. Pseudogenes are identified with disruptions in ORF (frameshift, early stop codon). Given that most pseudogenes ar…
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I'm using Infernal and RFAM to identify group II introns in gymnosperm mitochondria. Using `cmscan --mid --cut_ga --nohmmonly` it identifies 8 out of 16 family Intron_gpII ([RF00029](http://rfam.org/f…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/LieberInstitute/brainflowprobes
Confirm the follo…