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**Describe the issue**
Our lab is performing single nucleus analysis, I am trying to use Kallisto to pre-processing our data for RNA velosity analysis. My pipline is stucked at kb count step.
kb v…
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Hi Tobias:
In my experiment(1mM 4sU pulse for 30 min), before library construction, all the steps followed the standard protocol of SLAMseq, after total RNA extraction the rRNAs were removed from t…
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Dear author,
I want to get reads with various numbers of T2C conversions, such as 0, 1, 2, 3 T2Cs. So I used the content of sdunk file, ie. the output of alleyoop dump.
I wrote a simple script to c…
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I'm pretty sure all the executable paths are updated now for my configuration. Everything runs fine until I get to line 35 in 1_kallisto.smk (rule kb_velocity). I am getting the error below and am fin…
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Hi, I'm having trouble implementing the new sketch integration. Specifically, I am experiencing memory issues at different steps of the integration. My understanding was that BPCells and sketching met…
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Hi,
I am now using kb python to obtain splice/unsplice count from my 10X V3 single cell RNA sequencing data. It works but when I load the adata.h5ad file in the scVelo, I found that the barcodes i…
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**Describe the issue**
kb count of 1.6B 10X reads runs for days (run not completed yet) on a 16-thread computer. Based on my previous experience and the run time statement in your preprint, the run s…
dsb66 updated
4 months ago
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Hi all,
I am running Kallisto on bulk RNAseq data from ribo-depleted libraries. This means that my reads will include immature RNA with intronic reads. As such, I have assumed that the index shoul…
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We should make a thorough set of test documents to test the HTML and visual output of various LaTeXML features/packages. These can also be used to develop CSS in Storybook.
@dginev sent this advice…
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### Overview
We are encountering some issues in obtaining appropriate estimates of error rates; I believe these problems are coming from our new(-er) sequencing facility sending us fastq files contai…