عنوان

Hidden treasures in contemporary RNA sequencing /

(Number (ISBN

3030139735

(Number (ISBN

3030139743

(Number (ISBN

9783030139735

(Number (ISBN

9783030139742

Erroneous ISBN

3030139727

Erroneous ISBN

9783030139728

Title Proper

Hidden treasures in contemporary RNA sequencing /

General Material Designation

[Book]

First Statement of Responsibility

Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen.

Place of Publication, Distribution, etc.

Cham, Switzerland :

Name of Publisher, Distributor, etc.

Springer,

Date of Publication, Distribution, etc.

[2019]

Specific Material Designation and Extent of Item

1 online resource (v, 93 pages) :

Other Physical Details

illustrations (some color)

Series Title

SpringerBriefs in computer science,

ISSN of Series

2191-5768

Text of Note

Includes bibliographical references.

Text of Note

Intro; Contents; Hidden Treasures in Contemporary RNA Sequencing; Main Text; References

0

Text of Note

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.

Source for Acquisition/Subscription Address

Springer Nature

Stock Number

com.springer.onix.9783030139735

Title

Hidden treasures in contemporary RNA sequencing.

International Standard Book Number

9783030139728

Nucleotide sequence.

RNA.

Base Sequence.

Nucleotide sequence.

RNA.

COM014000

PSA

PSA

UB

Number

Edition

Class number

Book number

Class number

Mangul, Serghei

Eskin, Eleazar

Yang, Harry Taegyun

Zaitlen, Noah

Date of Transaction

20200823083421.0

Cataloguing Rules (Descriptive Conventions))

pn

Electronic name

[Book]

Y