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Hello everyone. First of all, I'd like to congratulate you on this incredible tool.
In my current project, I need to create cell x transcript matrices for my single nucleus human sample data genera…
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Hello,
when using Pizzly 0.37.3 (SeqAn 2.2.0) and Kallisto 0.43.1 with Ensembl 81 and one gets this error message from Pizzly:
```
Error, could not find any transcript sequences check that the i…
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Hi, I was looking into the above mentioned script (https://github.com/EnvGen/toolbox/blob/master/scripts/kallisto_concoct/input_table.py), and I was wondering about line 31:
```
kallisto_df['kalli…
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Hello,
I'm getting an error when trying to run croo after a successful run of the encode rna-seq-pipeline. My version of croo is 0.6.0
The command I ran is
`croo /storage/aadams/scripts/encode…
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Similar previous issues:
- https://github.com/pachterlab/kallisto/issues/399
- https://github.com/bioconda/bioconda-recipes/issues/42633
I thought that the release 0.50.1 should have fixed this, …
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We have a situation in which many of our samples have UMI and we'd like to deduplicate before running Kallisto. The question is, does kallisto require unsorted reads? Our STAR-aligned bams are positio…
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* sRNA analysis pipeline version: 3.6.2
* Python version: 3.10.9
* Operating System: Windows
### Description
I have used RNAlysis before, I was just trying to use the kallisto gene quantificat…
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perhaps a refactoring of the `fromfq` and `create_from_fastq` is overdue given the updates to kallisto, bustools, and kb wrapper.
- emprically, I am observing much greater memory usage from the loom…
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Hello,
I saw a few other Issues reported about "illegal instruction" behavior with kallisto index in version 0.50.
I don't think I have a problem with `kallisto index` (perhaps it was silent?), b…
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Hello,
the workflow ran almost through to the end. But the following Error occurred:
Error in rule diffexp_datavzrd:
jobid: 41
input: results/datavzrd/diffexp/model_X.yaml, results/ta…