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Hi, thanks for developing this great tool!
I believe a great addition to the workflow would be the possibility to provide a pre-annotated genome as input, allowing to:
1. speed up annotation for bat…
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### Ask away!
This is my first time running this workflow and my DGE analysis tsv files (for example results_dge.tsv) aren't incorporating the gene names in the gene_name column. Instead, the files d…
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- [ ] speed up addReadStats (big difference in the time between the different statistics - which ones should be calculated by default?)
- [ ] speed up filterReads (it's fine for small-ish sets of rea…
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Hi,
I recently ran Tiberius annotation on one of our insect genomes, utilizing the soft-masking model weights under CPU. I found that Tiberius performs faster than BRAKER3 in CPU mode, but the gene n…
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My code:
```r
bamba_ret = bambu(
reads = bam_file,
annotations = gtf_file,
genome = fna_file,
quant = FALSE
)
```
The error:
```
Error in value[[3L]](cond): Input g…
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Hi. This is not an issue just a question. Do you have a suggestion how can I convert the codan transcript base coding region annotation into a genome-based coding region annotation. This could be a bi…
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OverlapResolutions(genome_annotation = genome_annotation,
+ overlap_data = gene_overlaps, gene_pattern = c("Rik$", "^Gm"))
Error in seq.default(from = gene_B_exons[row_exonB, 1], …
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Hi, I really like this software in principal and am trying to get it to work! When I open the software I can load my files - I'd like to do this using gz files though, are fastq.gz files not supported…
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What am I doing incorrectly? I'm receiving this error message when I use an annotation file in my own disk:
Code:
```
gtf_file import -> FileForFormat
Execution halted
```
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Hi,
I am running copykat on my single cell data from mouse. It runs with no problems in all the samples except this one, which should be all tumor cells and I can´t understand why. My tumor cells h…