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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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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…
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IgBlast doesn't have a public bug ticket system (AFAIK) so I'm listing errors I've found here so people are aware of them. I will follow up with Jian @ NCBI about them.
I'm current testing with mou…
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Hi,
I was recommended by a JBrowse developer (**@cmdcolin**) to post this issue here:
[JBrowse Issue 1075](https://github.com/GMOD/jbrowse/issues/1075)
The issue is really around gff3 exporti…
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How do I access the exact human reference proteome dataset that is currently used by GO?
Is this it?
https://www.ebi.ac.uk/reference_proteomes
@Antonialock if so we should use this one, a…
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Place a warning flag on PRSS1 that there is a pseudogene that affects variant calls of these gene. We may want to expand this to cover other genes where this is a frequent issue. PMS2 has also come up…
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Hi there,
First, thank you for making this program; once it is working (for me), I think it will be a great tool. I am having a problem with the annotate portion however. Here is my script for run…
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Hi,
This is not an issue, more of a "query". I was wondering would it be possible to set a length threshold for the blastp, like the identity threshold.
I am applying this to look at the core ge…