kb_python

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kb count INDROPSV2 data, the result is not expected

1

**Describe the issue** kb count INDROPSV2 data [https://data.humancellatlas.org/explore/projects/7c75f07c-608d-4c4a-a1b7-b13d11c0ad31](https://data.humancellatlas.org/explore/projects/7c75f07c-608d-4c4a-a1b7-b13d11c0ad31) , Why does so much data generate only a little result? what other input files should I need? Thank you. Generating whitelist.txt...

monoplasty

# Patching CVE-2007-4559 Hi, we are security researchers from the Advanced Research Center at [Trellix](https://www.trellix.com). We have began a campaign to patch a widespread bug named CVE-2007-4559. CVE-2007-4559 is a...

TrellixVulnTeam

Error: Number of files (9) does not match number of input files required by technology 10XV3 (2)

5

**Describe the issue** kb_python 0.27.3 I get this error when trying to process the same batch of data, I don't know why this is happening? Hope to give some advice,...

monoplasty

Remove np.matrix dependency

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As most of us may know, `numpy` is slowly deprecating the `np.matrix` class. However, the package still has one dependency on this class in `report_matrix.ipynb`, and `scikit-learn` is also in...

JohnMMa

Syntax for 3-reads, paired end technology?

2

Hello, I am processing some DBiT-seq data (but the I guess the same applies to any combinatorial barcoding strategy) in which the R2 is composed by a spaced cell barcode,...

dawe

kb-python for MARS-seq

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Hi, I have been using kb-python to analyze scRNA-seq. first, thanks for creating such a user-friendly and useful tool. I appreciate it! I just had a technical issue when reanalyzing...

sam-shariati

No reads pseudoaligned in 10XV1 chemistry

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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...

XiaoMa55555

Issue obtaining unaligned reads

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I am interested in separating out my reads that are aligning and not aligning after using kb count. I modified kallisto so that the -n argument is passed. I then...

DanLesman

techno-sam

Potential problem with kb-python;

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**Describe the issue** I am executing this command as per 'box 2' in Nat. Biot. 2024 article: ~$ kb ref -i fpa_index.idx -g fpa_t2g.txt -f1 fpa_cdna.fasta cds_from_genomic.fasta genomic.gtf **What is...

fernando-pierucci-alves