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I ran loompy from fq using this command:
`loompy fromfq --threads 4 loom/R282_run1_Negative.loom R282_run1_Negative human_GRCh38_gencode.v31.600 datasheet.tsv R282_run1_Negative_L001_R1_001.fastq.gz …
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Hello,
I have RNA sequencing data prepared using rRNA depletion and would like to conduct gene-level differential expression analysis using p-value aggregation. In doing so, I attempted to exclude …
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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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Hello,
I am trying to annotate a reptilian genome that has a fairly good scaffolded assembly (N50 = ~215MB; 1,966 scaffolds). Genome busco completeness is ~93%
I have RNA-seq data from a pooled se…
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Reading a plaintext pseudoalignment from Themisto consumes a lot more memory than is necessary because plaintext input disables the internal encoding of the pseudoalignments as a sparse vector.
Wor…
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### Description of feature
The current nf-core/rnaseq (3.12.0) has initial steps to infer strandedness by first subsample fq, then Salmon to infer strandedness. This is an optional step and has led…
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Hello,
Thanks for your help on other threads. Version 0.48.0 supported an argument to quant to export a pseudoalignment BAM file, which is extremely useful. This has apparently been dropped. I'm wr…
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Hello,
I'm very interested in using kallisto as the alignment engine for some non-standard analyses using 10x data. I'd like to use kallisto to perform the pseudoalignments against custom reference…
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I'm trying to perform RNA velocity with kallisto, bustools and their wrapper kb-python following the instructions in [this R Notebook](https://bustools.github.io/BUS_notebooks_R/velocity.html). But I'…
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**Describe the issue**
I am running the latest version of kb_python to reproduce the example pipeline in the BIVI paper (which was using an older version of kb_python). I generated the loom successf…