Comments (8)
Also, another point of confusion for me is, is it not possible to use a gbk file with -- region parameter for different genomes, I have now manually annotated a gbk file. But when I want to apply it to another genome the --region parameter reports an error.
from bakta.
Hi, and sorry for responding late.
First: To take a deeper look into the first issue: Could you provide me with an example of this? genome in Fasta and both the raw/fixed gbk files?
Second: I'm not sure if I understand correctly what you're trying to achieve. You would like to re-use a Genbank file via --region
for another genome?
from bakta.
Hi, I have prepared the example data as requested:
s5.fasta
: The genome sequence annotated by PGAP pipeline.s5.gbk
: The raw GenBank file generated by PGAP fors5.fasta
contains genes not multiple of 3 in length.s5_edited.gbk
: The manually modified GenBank file where I removed the problematic genes so that Bakta's--region
parameter works correctly. Directly using--region s5.gbk
results in errors.1011.fasta
: Another genome sequence for which I would like to reuse the annotations froms5_edited.gbk
. However, this fails unless I manually change the first line ofs5_edited.gbk
froms5
to1011
, which is cumbersome.
Based on these observations, I would like to propose the following enhancements to Bakta:
- Automatically exclude or skip genes that are not multiples of 3 in length when using the
--region
parameter. - Reuse an annotated GenBank file for different genomes without manual modification of the file.
I have attached the example data for your review.
test.tar.gz
from bakta.
Related Issues (20)
- CRISPR position doesn't include last spacer
- circos legend HOT 1
- Reduce locus_tag offset from 5 to 1
- Color coding in bakta_plot --type cog HOT 2
- Inquiry about the coding density equation HOT 4
- Bakta run times on cluster HOT 4
- Downgrading dependencies is needed when installing bakta from conda HOT 2
- Roary is not working with bakta-generated gff3-files HOT 1
- KEGG annotations - the number is much lower number than expected HOT 4
- Possible issues running bakta in Singularity HOT 1
- Name and Product don't match Dbxref HOT 3
- tRNAscan-SE slow with multiple threads HOT 3
- PSC failed! diamond-error-code=-11 HOT 2
- Bakta Web Does Not Work HOT 6
- Diamond Error -9 HOT 3
- Is there a way to deactivate the overlap detection so bakta does not filter my input proteins? HOT 3
- Inquiry on CDS annotation HOT 2
- pyhmmer not found HOT 14
- pyrodigal has no attribute 'OrfFinder' HOT 11
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bakta.