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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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**Is your feature request related to a problem? Please describe.**
MSF relies on the order of the protein sequences in the faa files to identify systems. However, sometimes the proteins files downloa…
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Hi, okay, there is one additional FASTA that we want to include now. I have just added it to the Arabidopsis get_data.sh:
```
curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/arabido…
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Our kinase data also includes pseudogenes - are we including these? If so we have to think about why :)
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We must improve the way Apollo handles pseudogenes.
Currently, Apollo treats pseudogenes as separate entities with PARENT pseudogene and child transcript, and separate from any other isoforms of the…
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Hi, I have been using this pipeline and following the related publication in order to annotate pseudogenes in a new genome assembly project of a plant species. Having got the output from the pipeline,…
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Hi
Please does DFAST handle replicate pseudogenes in the case of stop codons that fragment genes and therefore generate multiple hits for a single gene.
Thanks
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Hi,
Apologies if this is in the documentation somewhere.
Is there an option in Stringtie to use a mask file (to ignore rRNA, pseudogenes etc?)
Many thanks.
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The software roary automatically exclude the very small genes and pseudogenes
https://github.com/sanger-pathogens/Roary/issues/367
https://github.com/sanger-pathogens/Roary/issues/288
Therefore, ge…
thkuo updated
6 years ago
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I was looking to use FlaGs with some user annotated genomes using the -l and -ld commands (using prokka).
I noticed that the way FlaGs parses GFF attributes seems to be hard-coded in so that local…