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Hi Brian,
I am using PASA to annotate a genome assembly following the PASA tutorial. The genome is ~500 MB and resulted in 400 contigs. EVM ran successfully and outputted 33k genes (with evidence f…
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Hello I am trying to run a non-model organism through TOBIAS ...
```
run_info:
organism: insect
```
I have added the genome size to macs
```
macs: "--gsize 222255331 --nomodel --shift…
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Hi,
I met a problem, the BUSCO score decrease after update.
The BUSCO v5 score was 91% after EVM (based peotein model).
Next,I performed PASA pipline to update my annotation with default parameter…
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### Operating System
Other Linux (please specify below)
### Other Linux
Rocky Linux release 8.9
### Workflow Version
v1.2.1
### Workflow Execution
Command line (Cluster)
### Other workflow exe…
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The following axioms should be created/updated from OMIM:
'has material basis in germline mutation in' some GENE
- gene-to-disease information from OMIM, based on rules discussed HERE (need to be…
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Hello,
I have 6 trinity fasta files, one for each tissue. How do I use all of this information PASA to get the genome annotation?
Would I run one of the fastas to create the database and then loa…
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The traceback:
```
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
FileNotFoundError: [Errno 2] No such file or directory: '/home/rstudio/workspace//data/SspArc0008_10x_c…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
v1.5.0
### Workflow Execution
EPI2ME Desktop (Local)
### Other workflow execution
_No response_
### EPI2M…
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We haven't looked at the annotation pipeline going into gene for a long time and it would be worth revisiting. For example, we are using vt to normalize and decompose, but we can likely achieve the sa…
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STATUS: DRAFT
Use case:Queries that can unify Gene expression/function/markers whether they are proteins, genes or transcripts.
TBD:
- Do we simply unify proteins/transcripts/genes or do we ma…