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| Exercise | Description | Completion |
| -------- | ------- | ------- |
| Q1A | Code present |YES |
| Q1B | `protein_coding` genes count correct | NO |
| Q1C | Discussion of interesting `biotyp…
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Does your Trust4 reference file for the human genome include pseudogenes? If not, do you have any idea on how I could include those genes in?
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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 there,
I've been running some annotation tests on DFAST for a collection of MAGs and I noticed that in some cases, the a huge number of partial pseudogenes being detected, sometimes close to 20% o…
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Hi Oliver,
We are interested in pseudogenes in a Salmonella genome. My colleague has run bakta, but no pseudogenes are being detected. This is unexpected based on some other analyses we have carrie…
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Hi TAs, I encountered a problem when running the **gatk Funcotator** in the annotation step.
The command line I use is:
```bash
gatk Funcotator --data-sources-path /lustre1/share/references/funco…
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Hi, Thank you for this awesome pipeline for pseudogenes analysis. I just wanted to know if I can get the fasta sequences categorized as Short, long, fragmented and intergenic sequences. Because, I thi…
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Hi! Thanks for the nice work!
Im wondering how exactly the summary statistics are calculated for the `id.txt` output file. I ran bakta on some paratuberculosis assemblies and when I check the summa…
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## Summary
There are a total of 31 V regions in the TCR Beta receptor locus. 11 of them are pseudogenes and 20 are transcribed genes (still need to confirm this). We only use primers for the 20 trans…