Evidence map›Paper›PMID 38045414›Full record

ArticlebioRxiv : the preprint server for biology2024

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.

Delaney K Sullivan, Kyung Hoi Joseph Min, Kristján Eldjárn Hjörleifsson, Laura Luebbert, Guillaume Holley, Lambda Moses, Johan Gustafsson, Nicolas L Bray, Harold Pimentel, A Sina Booeshaghi and 2 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Delaney K SullivanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.ORCID 0000-0002-8359-6705
Kyung Hoi Joseph MinGinkgo Bioworks, Boston, MA, 02210, USA.ORCID 0000-0003-0894-4017
Kristján Eldjárn HjörleifssonDepartment of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.ORCID 0000-0002-7851-1818
Laura LuebbertDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.ORCID 0000-0003-1379-2927
Guillaume HolleydeCODE Genetics/Amgen Inc., Reykjavik, Iceland.
Lambda MosesDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.ORCID 0000-0002-7092-9427
Johan GustafssonBroad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.ORCID 0000-0001-5072-2659
Nicolas L BrayBroad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.ORCID 0000-0002-4143-8194
Harold PimentelDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, 90095, USA.ORCID 0000-0001-8556-2499
A Sina BooeshaghiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.ORCID 0000-0002-6442-4502
Páll MelsteddeCODE Genetics/Amgen Inc., Reykjavik, Iceland.ORCID 0000-0002-8418-6724
Lior PachterDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.ORCID 0000-0002-9164-6231

Funding

Generation of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI NGAI, JOHN J. · 2017 to 2021
$64.7M
UCLA-Caltech Medical Scientist Training ProgramT32GM008042 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI AJIJOLA, OLUJIMI A, DAWSON, DAVID WAYNE · 1985 to 2023
$29.9M
Center for Mouse Genomic Variation at Single Cell ResolutionUM1HG012077 · NHGRI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Seyed Ali Mortazavi, BARBARA J WOLD · 2021 to 2026
$13.7M
NHGRI NIH HHS UM1 HG012077NIGMS NIH HHS T32 GM008042NIMH NIH HHS U19 MH114830
6 · The paper itself

Abstract

The term "RNA-seq" refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis that together can produce gene expression quantification from raw sequencing reads. The quantifications can be individualized for multiple cells, multiple samples, or both. Additionally, these tools allow gene expression values to be classified as originating from nascent RNA species or mature RNA species, making this workflow amenable to both cell-based and nucleus-based assays. This protocol describes in detail how to use kallisto and bustools in conjunction with a wrapper, kb-python, to preprocess RNA-seq data.

Identifiers

PMID38045414
PMCPMC10690192

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.