Hidden treasures in contemporary RNA sequencing / Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen.
Mangul, Serghei, author.; Yang, Harry Taegyun, author.; Eskin, Eleazar, author.; Zaitlen, Noah, author.
2019
QP625.N89 M36 2019
Available Online

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Title Hidden treasures in contemporary RNA sequencing / Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen.
Author Mangul, Serghei, author.
ISBN 9783030139735 (electronic book)
3030139735 (electronic book)
9783030139728
3030139727
DOI https://doi.org/10.1007/978-3-030-13973-5
Published Cham, Switzerland : Springer, [2019]
Language English
Description 1 online resource (v, 93 pages) : illustrations.
Other Standard Identifiers 10.1007/978-3-030-13973-5 doi
Call Number QP625.N89 M36 2019
Dewey Decimal Classification 572.8/633
Summary Advances in RNA-sequencing (RNA-seq) technologies have provided an unprecedented opportunity to explore the gene expression landscape across individuals, tissues, and environments by efficiently profiling the RNA sequences present in the samples. When a reference genome sequence or a transcriptome of the sample is available, mapping-based RNA-seq analysis protocols align the RNA-seq reads to the reference sequences, identify novel transcripts, and quantify the abundance of expressed transcripts. The reads that fail to map to the human reference, known as unmapped reads, are a large and often overlooked output of standard RNA-seq analyses. Even in carefully executed experiments, the unmapped reads can comprise a considerable fraction of the complete set of reads produced, and can arise due to technical sequencing produced by low-quality and error-prone copies of the nascent RNA sequence being sampled. Reads can also remain unmapped due to unknown transcripts, recombined B and T cell receptor sequences, A-to-G mismatches from A-to-I RNA editing, trans-splicing, gene fusion, circular RNAs, and the presence of non-host RNA sequences (e.g. bacterial, fungal, and viral organisms). Unmapped reads represent a rich resource for the study of B and T cell receptor repertoires and the human microbiome system--without incurring the expense of additional targeted sequencing. This book introduces and describes the Read Origin Protocol (ROP), a tool that identifies the origin of both mapped and unmapped reads. The protocol first identifies human reads using a standard high-throughput algorithm to map them onto a reference genome and transcriptome. After alignment, reads are grouped into genomic (e.g. CDS, UTRs, introns) and repetitive (e.g. SINEs, LINEs, LTRs) categories. The rest of the ROP protocol characterizes the remaining unmapped reads, which failed to map to the human reference sequences.
Bibliography, etc. Note Includes bibliographical references.
Access Note Access limited to authorized users.
Digital File Characteristics text file PDF
Source of Description Description based on online resource; title from digital title page (viewed on April 11, 2019).
Added Author Yang, Harry Taegyun, author.
Eskin, Eleazar, author.
Zaitlen, Noah, author.
Series SpringerBriefs in computer science.
Available in Other Form Print version: 9783030139728
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Intro; Contents; Hidden Treasures in Contemporary RNA Sequencing; Main Text; References

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