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There are so many different parameters when I run the flow of ORFS in different circuit, and different setting leads to different resulte. How do you set the parameters in you database in ORFS's confi…
Pxx-X updated
3 months ago
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Greeting! 👋
### Issue:
**GDS file generated by KLayout shows mismatches with the DEF file, leading to DRC violations in VIA ARRAY Cells (VIA-METAL1 and VIA-METAL2).**
both KLayout 0.28.8, 0.…
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ggggenomes allows to change position of orfs via
geom_feat(size = 3,position = "pile")
But how do I change the position of the genes in geom_gene() to make sure the ORF and genes allign?
posit…
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How Can I change the length parameter of predicted ORFs. I would like to specify sequences > 15bp, predict sequences larger than this size.
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### Subject
[Documentation] for documentation errors.
### Describe the bug
Our current submodule setup also requires the user to fork the OpenROAD repo for their fork of ORFS to be able to build.
…
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HI!
I've noticed that when you have an ORF that can't be annotated with any of the databases currently in set, pLannotate does not produce an CDS feature. Adding a custom database via the `-y` optio…
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Hello,
I've implemented function for plotting potential ORFs in 6-frame translation as ascii string.
It looks like this.
```
print(ascii_frameplot('ACATGTCAGTCGTGTGATCGTGTACGTCGATGATC', table=1…
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Hi,
Thank you for your tool. I am currently using FeGenie on contigs and have tried to use it on ORFs as well. My results are quite different and those for ORFs are incoherent. I have the impressi…
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I was wondering why Ribotricer does not have an ORF category that is called "internal". I was trying to compare results for ribotricer and ribocode and I identify an internal ORF in RiboCode that does…
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Hello again.
It appears that the final.ORFs file required for e.g. frameshift potential calculation is an empty file - I created annotation with create_annotation.sh script for yeast and human and i…