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Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS
RNA sequencing of single B cells provides simultaneous measurements of the cell state and its antigen specificity as determined by the B-cell receptor (BCR). However, to uncover the latter, further reconstruction of the BCR sequence is needed. We present BRAPeS (“BCR Reconstruction Algorithm for Pai...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Life Science Alliance LLC
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709718/ https://www.ncbi.nlm.nih.gov/pubmed/31451449 http://dx.doi.org/10.26508/lsa.201900371 |
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author | Afik, Shaked Raulet, Gabriel Yosef, Nir |
author_facet | Afik, Shaked Raulet, Gabriel Yosef, Nir |
author_sort | Afik, Shaked |
collection | PubMed |
description | RNA sequencing of single B cells provides simultaneous measurements of the cell state and its antigen specificity as determined by the B-cell receptor (BCR). However, to uncover the latter, further reconstruction of the BCR sequence is needed. We present BRAPeS (“BCR Reconstruction Algorithm for Paired-end Single cells” ), an algorithm for reconstructing BCRs from short-read paired-end single-cell RNA sequencing. BRAPeS is accurate and achieves a high success rate even at very short (25 bp) read length, which can decrease the cost and increase the number of cells that can be analyzed compared with long reads. BRAPeS is publicly available at the following link: https://github.com/YosefLab/BRAPeS. |
format | Online Article Text |
id | pubmed-6709718 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Life Science Alliance LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-67097182019-09-06 Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS Afik, Shaked Raulet, Gabriel Yosef, Nir Life Sci Alliance Methods RNA sequencing of single B cells provides simultaneous measurements of the cell state and its antigen specificity as determined by the B-cell receptor (BCR). However, to uncover the latter, further reconstruction of the BCR sequence is needed. We present BRAPeS (“BCR Reconstruction Algorithm for Paired-end Single cells” ), an algorithm for reconstructing BCRs from short-read paired-end single-cell RNA sequencing. BRAPeS is accurate and achieves a high success rate even at very short (25 bp) read length, which can decrease the cost and increase the number of cells that can be analyzed compared with long reads. BRAPeS is publicly available at the following link: https://github.com/YosefLab/BRAPeS. Life Science Alliance LLC 2019-08-26 /pmc/articles/PMC6709718/ /pubmed/31451449 http://dx.doi.org/10.26508/lsa.201900371 Text en © 2019 Afik et al. https://creativecommons.org/licenses/by/4.0/This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Methods Afik, Shaked Raulet, Gabriel Yosef, Nir Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS |
title | Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS |
title_full | Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS |
title_fullStr | Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS |
title_full_unstemmed | Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS |
title_short | Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS |
title_sort | reconstructing b-cell receptor sequences from short-read single-cell rna sequencing with brapes |
topic | Methods |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709718/ https://www.ncbi.nlm.nih.gov/pubmed/31451449 http://dx.doi.org/10.26508/lsa.201900371 |
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