Bioinformatics Tools for Next-Generation RNA Sequencing Analysis. Marconi, M., Rodriguez-Romero, J., Sesma, A., & Wilkinson, M., D. Sesma, A. & von der Haar, T., editors. Fungal RNA biology, pages 371-391. Springer International Publishing, 2014. ![Fungal RNA biology [link]](https://bibbase.org/img/filetypes/link.svg "link")
Website doi abstract bibtex 1 download The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools.
@inbook{
type = {inbook},
year = {2014},
pages = {371-391},
websites = {http://link.springer.com/chapter/10.1007/978-3-319-05687-6_15},
publisher = {Springer International Publishing},
chapter = {Bioinformatics Tools for Next-Generation RNA Sequencing Analysis},
id = {8a36acd0-ce7f-3168-b83d-2da0a2c5f4bb},
created = {2014-07-02T09:11:39.000Z},
file_attached = {false},
profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},
last_modified = {2017-03-22T07:45:59.566Z},
read = {false},
starred = {false},
authored = {true},
confirmed = {true},
hidden = {false},
citation_key = {Marconi2014},
private_publication = {false},
abstract = {The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools.},
bibtype = {inbook},
author = {Marconi, Marco and Rodriguez-Romero, Julio and Sesma, Ane and Wilkinson, Mark D.},
editor = {Sesma, Ane and von der Haar, T.},
doi = {10.1007/978-3-319-05687-6_15},
title = {Fungal RNA biology}
}
Downloads: 1
{"_id":"gpeGC3pxcRB543aAT","bibbaseid":"marconi-rodriguezromero-sesma-wilkinson-fungalrnabiology-2014","authorIDs":["3D2gJyDWo9oBKnSCp","SDCtrmyrMaghAhukd"],"author_short":["Marconi, M.","Rodriguez-Romero, J.","Sesma, A.","Wilkinson, M., D."],"bibdata":{"type":"inbook","year":"2014","pages":"371-391","websites":"http://link.springer.com/chapter/10.1007/978-3-319-05687-6_15","publisher":"Springer International Publishing","chapter":"Bioinformatics Tools for Next-Generation RNA Sequencing Analysis","id":"8a36acd0-ce7f-3168-b83d-2da0a2c5f4bb","created":"2014-07-02T09:11:39.000Z","file_attached":false,"profile_id":"17c87d5d-2470-32d7-b273-0734a1d9195f","last_modified":"2017-03-22T07:45:59.566Z","read":false,"starred":false,"authored":"true","confirmed":"true","hidden":false,"citation_key":"Marconi2014","private_publication":false,"abstract":"The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools.","bibtype":"inbook","author":"Marconi, Marco and Rodriguez-Romero, Julio and Sesma, Ane and Wilkinson, Mark D.","editor":"Sesma, Ane and von der Haar, T.","doi":"10.1007/978-3-319-05687-6_15","title":"Fungal RNA biology","bibtex":"@inbook{\n type = {inbook},\n year = {2014},\n pages = {371-391},\n websites = {http://link.springer.com/chapter/10.1007/978-3-319-05687-6_15},\n publisher = {Springer International Publishing},\n chapter = {Bioinformatics Tools for Next-Generation RNA Sequencing Analysis},\n id = {8a36acd0-ce7f-3168-b83d-2da0a2c5f4bb},\n created = {2014-07-02T09:11:39.000Z},\n file_attached = {false},\n profile_id = {17c87d5d-2470-32d7-b273-0734a1d9195f},\n last_modified = {2017-03-22T07:45:59.566Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {true},\n hidden = {false},\n citation_key = {Marconi2014},\n private_publication = {false},\n abstract = {The purpose of this chapter is to introduce the reader to some of the most popular bioinformatics tools and resources available for RNA analysis. The introduction of RNA next-generation sequencing led to an explosion in the amount of quantitative transcript sequence data, which necessitated the development of adequate tools to process and make a sense of these rich and complex datasets. A large number of programs, platforms, and databases dedicated to RNA analysis have been produced over the past approximately 20 years; however, like so much other bioinformatics software, only a small portion of them are still available and in-use. As such, we will focus only on those tools and applications still in common use. This chapter is composed of three sections: the description of the general protocols for RNA sequence (generically called RNA-Seq) analyses, an outline of the most common approaches to map polyadenylation sites, and a brief introduction to noncoding RNA (ncRNA) analysis. The first section will describe the composition of steps within a typical RNA-Seq study: the experimental design, the sequencing methods, the data quality control, the read mapping, and the differential expression analysis. The second section will introduce a few recent methods developed to map polyadenylation sites: the experimental protocols (which are variations of RNA-Seq), polyadenylation site databases and prediction programs, and cis-regulatory elements discovery. The third and final section will present several of the ncRNA databases and prediction tools.},\n bibtype = {inbook},\n author = {Marconi, Marco and Rodriguez-Romero, Julio and Sesma, Ane and Wilkinson, Mark D.},\n editor = {Sesma, Ane and von der Haar, T.},\n doi = {10.1007/978-3-319-05687-6_15},\n title = {Fungal RNA biology}\n}","author_short":["Marconi, M.","Rodriguez-Romero, J.","Sesma, A.","Wilkinson, M., D."],"editor_short":["Sesma, A.","von der Haar, T."],"urls":{"Website":"http://link.springer.com/chapter/10.1007/978-3-319-05687-6_15"},"biburl":"https://bibbase.org/service/mendeley/17c87d5d-2470-32d7-b273-0734a1d9195f","bibbaseid":"marconi-rodriguezromero-sesma-wilkinson-fungalrnabiology-2014","role":"author","metadata":{"authorlinks":{"wilkinson, m":"https://bibbase.org/service/mendeley/17c87d5d-2470-32d7-b273-0734a1d9195f"}},"downloads":1},"bibtype":"inbook","creationDate":"2020-07-27T17:40:08.564Z","downloads":1,"keywords":[],"search_terms":["fungal","rna","biology","marconi","rodriguez-romero","sesma","wilkinson"],"title":"Fungal RNA biology","year":2014,"biburl":"https://bibbase.org/service/mendeley/17c87d5d-2470-32d7-b273-0734a1d9195f","dataSources":["u3DebWvhQaEque62E","ya2CyA73rpZseyrZ8","2252seNhipfTmjEBQ"]}