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Hello!
I got MetaCerberus to work, I'm using the third (annotation) part of the pipeline, inputting combined prokaryotic, eukaryotic and viral gene predictions predicted with different programmes. …
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TL;DR - there are uniprot KW and EC annotations to this family that contradict the literature.
I'll take yeast RAD26 as an exemplar here, but similar patterns are seen in orthologs.
Uniprot has …
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i am seeing the error:
```
Error, cmd: bash -c "set -euxo pipefail; cat /refbuild/GRCh37/starfusion/../annotation/Homo_sapiens.GRCh37.75.gtf | egrep 'IG_V_gene|IG_C_gene|IG_D_gene|IG_J_gene' | awk '…
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Hi,
I have different InterProScan results between running GAAS and running InterProScan manually, with the same input files.
I do not see any difference in the input arguments. As you know the bac…
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Hello,
After running PASA annotation update pipeline, I have the updated annotation output in the GFF3 format. I am interested in understanding the specific updates made by PASA in original gene mode…
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### Description of the bug
Hi Edmund,
I am raising a ticket here for the strand-flipping issue I mentioned on slack.
Bug:
BigWigs generated for PROseq samples appear to be flipped. The strand ca…
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Hello,
I have been working with scGPT for the last week and I am studying currently the GRN part. By running the Tutorial_GRN notebook, and downloading the data/model in the links provided, I am un…
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**Describe the bug**
Run ends with error due to a missing scipy import. I'm running a WGS trio from Illumina DRAGEN pipeline through Cravat with ClinVar, case-control, and SpliceAI modules.
**To …
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When I try to run the map_leafcutter_cluster_to_gene part for post-processing, it gives me this error..
```
FATAL: could not open image /restricted/projectnb/casa/xqtl-pipeline/container/singul…
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While using Bakta, I realized that one of the known genes was not predicted. However, both Prokka and PGAP accurately predicted the gene. I tried using the -region option for this. Although Prokka's g…