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I think it might make sense to replace kallisto with this tool: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08278-7
We could reduce the size of the proteome predicted by transde…
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When you input multiple FASTQ files into the `kb count` function, does it process them sequentially or is there a way to parallelize it? Especially because for me, the first step "kallisto bus" takes …
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Hello, I'm having an error that i cant understand when trying to get my count matrix with kb count:
$ kb count -i index.idx -g t2g.txt -t 15 --em --filter --loom -o out_em_algorithm_filter/ -x 10XV…
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Hi,
I have been following this tutorial on generating spliced and unspliced matrices for RNA velocity analysis: https://bustools.github.io/BUS_notebooks_R/velocity.html#generate_spliced_and_unsplic…
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Hello - not sure what I am doing wrong to get this error despite providing all necessary files in correct format with correct arguments.
After running pizzly, I get "pizzly: Not enough arguments wer…
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Hello,
I am getting an error while indexing of the BAM files. I have installed the tool using conda. So the kallisto version is at 0.44 as mentioned. Below is STDOUT
```
Results stored in: stra…
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Hello,
I was wondering about the annotation version you were using for processing mouse experiments using Kallisto. Ensembl 90 annotation has 131,195 unique transcripts; however, the cDNA file you…
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This needs to be included since Kallisto can estimate fragment length from paired-end reads but not from single-end reads.
This fragment length notion is a bit confusing but comes from the Conuts/F…
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Hi there,
So I'm having a small issue that I can't quite seem to find an answer for. I've successfully built the index and I'm now trying to use the quant function by invoking the following:
```
…
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Do you guys have any plans to add an annotation pipeline to the transcriptome (like through Trinotate). I am struggling with that portion of the analysis and really like the snakemake workflows you g…