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Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.
Dong, Xueyi; Du, Mei R M; Gouil, Quentin; Tian, Luyi; Jabbari, Jafar S; Bowden, Rory; Baldoni, Pedro L; Chen, Yunshun; Smyth, Gordon K; Amarasinghe, Shanika L; Law, Charity W; Ritchie, Matthew E.
Afiliação
  • Dong X; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. dong.x@wehi.edu.au.
  • Du MRM; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia. dong.x@wehi.edu.au.
  • Gouil Q; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
  • Tian L; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
  • Jabbari JS; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
  • Bowden R; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
  • Baldoni PL; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
  • Chen Y; Guangzhou National Laboratory, Guangzhou, China.
  • Smyth GK; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
  • Amarasinghe SL; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
  • Law CW; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
  • Ritchie ME; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
Nat Methods ; 20(11): 1810-1821, 2023 Nov.
Article em En | MEDLINE | ID: mdl-37783886
ABSTRACT
The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflows. Here, we present a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together with synthetic, spliced, spike-in RNAs (sequins). Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that StringTie2 and bambu outperformed other tools from the six isoform detection tools tested, DESeq2, edgeR and limma-voom were best among the five differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the five tools compared, which suggests further methods development is needed for this application.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Sequenciamento de Nucleotídeos em Larga Escala Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article