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Hello!
I'm having a slight issue with the annotations generated by EGAPx. When I translate the CDS into a protein sequence, I'm seeing a lot of premature stop codons. This is a species where I am s…
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@joshkh Can you take a look at component 400 for me?
Specifically this count:
https://github.com/intermine/intermine/blob/dev/intermine/webapp/main/resources/webapp/bagUploadConfirm.jsp#L53
For…
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When genbanks are used as input that still have windows/dos line-endings, cds-extractor.pl just quits without an error message, giving the impression that it successfully extracted all CDS.
Maybe i…
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Hi all,
I was wondering how augustus distinguishes between internal stop codons that represent 'true' pseudogenization as opposed to something going wrong with characterising the boundaries of gene…
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Dear All,
I was parsing a genbank file (more precisely a gbff file (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/365/GCF_000009365.1_ASM936v1/GCF_000009365.1_ASM936v1_genomic.gbff.gz)) and du…
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There is a [new collection](https://rvs.u.hpc.mssm.edu/divas/) of background panels out; it would be nice to have their variants annotated in GEMINI.
> The Disease Variant Store provides information …
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I found that the file of all HHyeast hits (HHpry_hits_171010) hd nothing from a particular ORF in it. Also that ORF is shown by HHyeast as "does not exist" Yet I have the file which was made by HHyeas…
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It looks like all IGH fusions are missed. IGH fusions are for example found in lymphoblastic leukemias.
For example, the IGH-DUX4 fusion is missed in NALM-6 cell line (using this RNA-seq data from…
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Hi,
I was wondering if there was a way to make the static plot for two separate sequences? As I understand it right now, it checks the identity of a sequence with itself.
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| Exercise | Description | Completion |
| -------- | ------- | ------- |
| Q1A | Code present | Yes |
| Q1B | `protein_coding` genes count correct | Yes |
| Q1C | Discussion of interesting `biotyp…