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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
- Acacia/crassicarpa/genomes/Acra3RX.gnm1.YX4L
- Acacia/crassicarpa/annotations/Acra3RX.gnm1.ann…
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# Main steps for adding new genome and annotation collections
### Genus/species:
name: New genomes+annotations checklist
description: Checklist of tasks associated with new genome and annotati…
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### Description of the bug
Hi am working with the pipeline, in the test working fine. with samples do not report the VARIANT_CALLING, there is no error in the run.
How I can make that processes?
##…
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Hi,
I encountered a problem when running **EpiTraceAge_Convergence** in the step 4 of the [tutorial](https://epitrace.readthedocs.io/en/latest/MSscATAC.html#step-4-epitrace-analysis). It seems to b…
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# OGS remapping
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# manual annotation remapping
- [ ] request whole-genome alignment
- [ …
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Suppose I'm trying to obtain annotation data for Plasmodium vivax (GCF_000002415.2). If I download data from NCBI datasets and do a simple grep on sequence headers, I get this:
```
>NC_009906.1 Plas…
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## Describe the issue
VEP performed incorrect pHGVS annotation for the variant `NM_173660.5:c.1124_1127dup (rs606231128)` .
VEP annotated the variant as `NP_775931.3:p.Ala377ProfsTer31` when the cor…
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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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Hi all,
I am running STAR-Fusion with all filters removed from a docker container on a single chimeric.out.junction file with this command:
```
docker run -v $(pwd):$(pwd) \
-v ${ctat_lib_di…
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Hi,
I am trying to generate sashimi plots using BAM files made from running rMATS on FASTQ files. I am using two files that hold my replicates.
My run:
python /Packages/rmats2sashimiplot/src/rm…