Abstract
The transcAnalysis pipeline is a comprehensive tool that allows the analysis of transcriptome data. The pipeline allows for analysis of differential expression, alternative splicing, lncRNA and RNA editing analysis, with a specific focus on A-to-I editing mediated by the ADAR protein. This type of RNA editing is widespread and can significantly affect gene regulation and function. The results from these analyses are integrated, and the events are associated with each gene. The pipeline also integrates results that can help correlate gene expression and post-transcriptional events. This allows for a comprehensive understanding of the functional impact and provides insight into the biological processes and pathways associated with these events. One of the significant advantages of the transcAnalysis pipeline is its ability to perform all these analyses with a single command using the Snakemake package. This feature simplifies the analysis process and makes it accessible to researchers with limited bioinformatics expertise. Its user-friendly ability to perform multiple analyses with a single command make it an ideal choice for researchers looking to analyze transcriptome data.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hardwick, S., Deveson, I., Mercer, T.: Reference standards for next-generation sequencing. Nat. Rev. Genet. 18(8), 473–484 (2017)
Marasco, L.E., Kornblihtt, A.R.: The physiology of alternative splicing. Nat. Rev. Mol. Cell Biol. 24(4), 242–254 (2023)
Song, B., Shiromoto, Y., Minakuchi, M., Nishikura, K.: The role of RNA editing enzyme ADAR1 in human disease. WIRES 13(1), e1665 (2023)
Mölder, F., et al.: Sustainable data analysis with Snakemake. F1000Res 18, 10–33 (2021)
Love, M.I., Huber, W., Anders, S.: Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 15(12), 550 (2014)
Shen, S., et al.: rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc. Natl. Acad. Sci. U.S.A. 111(51), E5593–E5601 (2014)
Zhang, F., Lu, Y., Yan, S., Xing, Q., Tian, W.: SPRINT: an SNP-free toolkit for identifying RNA editing sites. Bioinformatics 33(22), 3538–3548 (2017)
Han, J., et al.: LncRNAs2Pathways: identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. Sci. Rep. 7, 46566 (2017)
Gillespie, M., et al.: The Reactome pathway knowledgebase 2022. Nucleic Acids Res. 50(D1), D687–D692 (2022)
Mishra, G.R., et al.: Human protein reference database-2006 update. Nucleic Acids Res. (34), D411–D414 (2006)
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., Morishima, K.: KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45(D1), D353–D361 (2017)
Nishimura, D.: BioCarta. Biotech Softw. Internet Rep. 2(3), 117–120 (2001)
Dobin, A., et al.: STAR: ultrafast universal RNA-Seq aligner. Bioinformatics 29(1), 15–21 (2013)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Barros, P.H.A., Silva, W.M.C., Brigido, M.M. (2023). transcAnalysis: A Snakemake Pipeline for Differential Expression and Post-transcriptional Modification Analysis. In: Reis, M.S., de Melo-Minardi, R.C. (eds) Advances in Bioinformatics and Computational Biology. BSB 2023. Lecture Notes in Computer Science(), vol 13954. Springer, Cham. https://doi.org/10.1007/978-3-031-42715-2_10
Download citation
DOI: https://doi.org/10.1007/978-3-031-42715-2_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-42714-5
Online ISBN: 978-3-031-42715-2
eBook Packages: Computer ScienceComputer Science (R0)