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I am using singularity to run this pipeline.
Unable to download requested sequence data from Ensembl (ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.…
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### Describe the bug
After I clicked "Start Kallisto quantify (paired-end reads)", I encountered the error message below:
Traceback (most recent call last):
File "rnalysis/gui/gui.py", line 44…
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Die Felder für Werkverzeichnisse (heute 690) und alternative Titel (heute 730) wurden nicht vollständig migriert.
https://muscat.rism.info/admin/sources/451502054
Nur die ersten 10 Instanzen dieser…
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Version: `kallisto 0.51.1`
I'm following a workflow outlined in [issue 456](https://github.com/pachterlab/kallisto/issues/456) for using lr-kallisto with bulk ONT. `kallisto bus`, `bustools sort`, …
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Hi, thanks for producing this great software. I've a suggestion to add a check of user input.
The documentation states "The default running mode is paired-end and requires an even number of FASTQ f…
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When running `conda env create -f environment.yml` I got this error:
```
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- samtools==1.19…
arusa updated
3 months ago
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Hi,
thank you for your help. I successfully ran BayesDRIMSeq for kallisto and salmon counts. However, when I tried in RSEM calculated counts, I encountered the following error:
Error in { : task…
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Hello,
I was wondering if it is more appropriate to use the v1 standard kallisto index https://github.com/pachterlab/kallisto-transcriptome-indices/releases for bulk RNA seq data compared to an ind…
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Hi,
@warrenmcg's advice in Issue #201 to subset files (below) does not work for me
> kal
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Hi there
We are having trouble using the newer versions of Kallisto, mainly all versions >=0.50.0 with the new index. Here is what I'm doing:
```bash
$ ./kallisto_0.50.1.sif kallisto index -i t…