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The BUS Format for Single-Cell RNA-Seq Processing and Analysis

Gao, Fan and da Veiga Beltrame, Eduardo and Gehring, Jase A. and Hjoerleifsson, Kristin E. Edljarn and Lu, Lambda and Melsted, Paull and Ntranos, Vasilis and Pachter, Lior and Svensson, Valentine (2019) The BUS Format for Single-Cell RNA-Seq Processing and Analysis. Journal of Biomolecular Techniques, 30 (S1). S62. ISSN 1524-0215. PMCID PMC6938108. https://resolver.caltech.edu/CaltechAUTHORS:20200106-081503232

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Abstract

The Barcode-UMI-Set format (BUS) is a recently developed format for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with most single-cell RNA-seq technologies, can be generated efficiently, and allows for development of modular and robust workflows for processing and analysis of single-cell RNA-seq reads. To demonstrate the utility of BUS, we processed 381,992,071 single-cell RNA-Seq reads from a 1:1 mixture of fresh frozen human cells (HEK293T) and mouse cells (NIH3T3) produced with 10x technology and hosted on the 10x Genomics website. The generation of BUS format using a new command in the kallisto program took 984 seconds for this data (in comparison with 55,745 seconds with the 10x Genomics CellRanger software). I will present results showing that this workflow not only produces comparable results to the existing standard workflow, but is flexible and useful for many other applications.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://jbt.abrf.org/jbt-static/index.cfm/page/archives/jbt_archive.htmPublisherJournal Issue
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6938108PubMed CentralArticle
ORCID:
AuthorORCID
da Veiga Beltrame, Eduardo0000-0002-1529-9207
Lu, Lambda0000-0002-7092-9427
Melsted, Paull0000-0002-8418-6724
Ntranos, Vasilis0000-0002-2477-0670
Pachter, Lior0000-0002-9164-6231
Svensson, Valentine0000-0002-9217-2330
Additional Information:© 2019 Association of Biomolecular Resource Facilities. Presenter: Fan Gao. This is joint work with Eduardo da Veiga Beltrame, Jase A. Gehring, Kristj¡n E. Edljarn Hjoerleifsson, Lambda Lu, Paull Melsted, Vasilis Ntranos, Lior Pachter, and Valentine Svensson.
Issue or Number:S1
PubMed Central ID:PMC6938108
Record Number:CaltechAUTHORS:20200106-081503232
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200106-081503232
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:100522
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Jan 2020 19:33
Last Modified:09 Mar 2020 13:19

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