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Hi,
I am trying to assess mitochondrial gene expression. I downloaded the fasta and the gff3 from NCBI.
[(https://www.ncbi.nlm.nih.gov/nuccore/BK063639.1](url)
Since NCBI doesn't have the gtf, I us…
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### DB Selector
DB3K
### Affected DBID(s)
sensor 4964, sensor 4156, sensor 5955
### Summary of Changes
**_-9M96DM seeker to J band, add HOJ (sensor 4964) Agat 9B-1103M-200PS_
-R-77-1 / …
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Another way we discussed to assess annotation quality is to look at overlapping genes, sense and antisense.
You would expect that similar genomes would have the same rate of these classes, if not, t…
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Hi!
I am using the singularity on school's computation cluster. After building the sif image of AGAT-1.4.1, I had an error. The processes is shown below:
```bash
$module load singularity/3.11.3
…
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**Describe the bug**
I lifted annotations from a reference genome to another isolate with LiftOff. I wanted to check how the new annotations are. Do they have start and stop codons or in-frame/premat…
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**agat_sp_merge_annotations.pl output incompatible with cellranger**
I have two gff files I want to merge.
One is an old annotation, and the other is a new annotation I have just made using brake…
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Hello!
I'm trying to add introns to my GFF file using the command agat_sp_add_introns.pl --gff MY.gff --out MY_introns.gff
Unfortunately, I got the below error. I also tried using the commands …
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**Describe the bug**
I installed `agat` using conda with `-c bioconda`. However, the resulting agat_sp_filter_feature_by_attribute_value.pl is an old version.
**General (please complete the follow…
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When running ``genomeqc`` on ``assests/samplesheet.csv`` (bees and wasps) BUSCO fails on the SEPP step with this warning message:
```
Placements failed. Try to rerun increasing the memory or select a…
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**Describe the bug**
When running the command, it gets towards the bottom of the process but then errors saying the it could not open the index file. This is a resulting GFF file from MAKER output.
…