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CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin

Distinguishing circular RNA reads from reads derived from the linear host transcript is a challenging task because of sequence overlap. We developed a computational approach, CiLiQuant, that determines the relative circular and linear abundance of transcripts and gene loci using back-splice and unam...

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Autores principales: Morlion, Annelien, Hulstaert, Eva, Vromman, Marieke, Anckaert, Jasper, Everaert, Celine, Vandesompele, Jo, Mestdagh, Pieter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580843/
https://www.ncbi.nlm.nih.gov/pubmed/36304262
http://dx.doi.org/10.3389/fbinf.2022.834034
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author Morlion, Annelien
Hulstaert, Eva
Vromman, Marieke
Anckaert, Jasper
Everaert, Celine
Vandesompele, Jo
Mestdagh, Pieter
author_facet Morlion, Annelien
Hulstaert, Eva
Vromman, Marieke
Anckaert, Jasper
Everaert, Celine
Vandesompele, Jo
Mestdagh, Pieter
author_sort Morlion, Annelien
collection PubMed
description Distinguishing circular RNA reads from reads derived from the linear host transcript is a challenging task because of sequence overlap. We developed a computational approach, CiLiQuant, that determines the relative circular and linear abundance of transcripts and gene loci using back-splice and unambiguous forward-splice junction reads generated by existing mapping and circular RNA discovery tools.
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spelling pubmed-95808432022-10-26 CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin Morlion, Annelien Hulstaert, Eva Vromman, Marieke Anckaert, Jasper Everaert, Celine Vandesompele, Jo Mestdagh, Pieter Front Bioinform Bioinformatics Distinguishing circular RNA reads from reads derived from the linear host transcript is a challenging task because of sequence overlap. We developed a computational approach, CiLiQuant, that determines the relative circular and linear abundance of transcripts and gene loci using back-splice and unambiguous forward-splice junction reads generated by existing mapping and circular RNA discovery tools. Frontiers Media S.A. 2022-02-22 /pmc/articles/PMC9580843/ /pubmed/36304262 http://dx.doi.org/10.3389/fbinf.2022.834034 Text en Copyright © 2022 Morlion, Hulstaert, Vromman, Anckaert, Everaert, Vandesompele and Mestdagh. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Bioinformatics
Morlion, Annelien
Hulstaert, Eva
Vromman, Marieke
Anckaert, Jasper
Everaert, Celine
Vandesompele, Jo
Mestdagh, Pieter
CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
title CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
title_full CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
title_fullStr CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
title_full_unstemmed CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
title_short CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin
title_sort ciliquant: quantification of rna junction reads based on their circular or linear transcript origin
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9580843/
https://www.ncbi.nlm.nih.gov/pubmed/36304262
http://dx.doi.org/10.3389/fbinf.2022.834034
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