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I have downloaded the SHARE-seq [ATAC-seq](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4156597) data and trying to create ChromatinAssay object:
```{r, eval=FALSE}
atac
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Hi,
I'm trying to do a prediction based on RNASeq data. The hintsfile.gff was successfull created by the pipeline and GeneMark-ES/ET is called. But when the call of `parse_ET.pl --section ET_A /G…
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I was wondering ... if it is advisable to use a pangenome file instead of genomes. Technically it works, but: does it make biological sense to do this?.
Thanks in advance.
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Hello,
We (myself and @Al-Murphy) use `VariantAnnotation` in our package [`MungeSumstats`](https://github.com/neurogenomics/MungeSumstats) and are looking for a way to efficiently convert the (col…
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**Related To**
- [x] Bactopia
- [ ] Bactopia Tools
**Is this related to a problem?**
Kind of: while downstream analysis of the main Bactopia pipeline is supposed to be carried out with Bactopi…
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Hello, I am using this command in a loop to parse through multiple paired files. This might be a coding error on my part but my loops are only generating the .domtblout file and not the padloc.csv/gff…
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### **Q1:** Getting Execution halted in `mocha_plot.R` script
Command:
```
mocha_plot.R --mocha --stats $dir/$pfx.stats.tsv --vcf $dir/$pfx.bdev.bcf --png MH0145622.png --cytoband $cyto…
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Hello,
when running FragPipe in headless mode (analyzing a TMT experiment), I get weird TMT channel names. I put an example here: https://oc.embl.de/index.php/s/9iEiAtMw6j0hSMK
In the annotatio…
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Hi!
MicrobeAnnotator looks very cool! However, I haven't been able to build the database. I installed MicrobeAnnotator via conda, then attempted to build database (the light version) with:
micr…
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GT-pro version: 1.0.1
python version: 3.10.1
Hi,
While running GT-pro optimise with example fastq file SRR413665_2.fastq.gz, program returned those error messages as below.
`bash /home/…
boaty updated
2 years ago