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Hello, I am setting up FVE to run for the first time. Thank you for creating this program, I am excited about its utility! On my first attempt to run the test data set, I got this error:
(base) : …
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Hi,
I am using the 0.48.0 version of kallisto, as well as bustools (0.41.0) to demultiplex and obtain gene count tables for my BD Rhapsody WTA data. This is my initial kallisto bus script:
**kallis…
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After calculating abundance estimates, if the user as selected cleanup, the script deletes the downloaded fastq files. I noticed that there is no check if the `kallisto` completed successfully or not.…
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Hi,
I got the following error message from kallisto quant, but kallisto seems to be on version 0.50.0 and it doesn't explain what those versions refer to.
```
[quant] fragment length distributio…
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Are there plans to support Salmon or Kallisto for expression filtering, instead of using RSEM?
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Hi everyone, I had an issue related to output. I installed kallisto v0.44, python 3.12, RSeQC. I tried to run check_strandedness for samples given by kallisto as demo. However, there was no informatio…
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See #36
- [Colab: basics.ipynb](https://colab.research.google.com/github/pachterlab/kallistobustools/blob/master/notebooks/basic.ipynb#scrollTo=XWS-gw-uieMC)
- [Modular and efficient pre-processi…
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Hello,
I am working with bulk RNA seq data. I created a reference like shown below:
`kallisto index -i mouse_version111cdna Mus_musculus.GRCm39.cdna.all.fa.gz`
Then I created a t2g file using…
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Dear team,
I'm a little bit confused about the build index step. The manual says that it builds a transcriptome index but needs as input a genomic fasta and a gff. I would like to create the count…
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Hello, Sleuth team @warrenmcg @pimentel
I've been using Kallisto and Sleuth for a short while, and it works well for me, so thank you for these tools!
I do want to confirm that I'm running Sleu…