Language:
English
繁體中文
Help
Login
Back
Switch To:
Labeled
|
MARC Mode
|
ISBD
Hidden Treasures in Contemporary RNA...
~
Yang, Harry Taegyun.
Hidden Treasures in Contemporary RNA Sequencing
Record Type:
Language materials, printed : Monograph/item
Title/Author:
Hidden Treasures in Contemporary RNA Sequencing/ by Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen.
Author:
Mangul, Serghei.
other author:
Yang, Harry Taegyun.
Description:
V, 93 p. 49 illus., 48 illus. in color.online resource. :
Contained By:
Springer Nature eBook
Subject:
Bioinformatics. -
Online resource:
https://doi.org/10.1007/978-3-030-13973-5
ISBN:
9783030139735
Hidden Treasures in Contemporary RNA Sequencing
Mangul, Serghei.
Hidden Treasures in Contemporary RNA Sequencing
[electronic resource] /by Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen. - 1st ed. 2019. - V, 93 p. 49 illus., 48 illus. in color.online resource. - SpringerBriefs in Computer Science,2191-5768. - SpringerBriefs in Computer Science,.
Abstract -- Main Text -- Acknowledgement -- Disclosure -- References.
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.
ISBN: 9783030139735
Standard No.: 10.1007/978-3-030-13973-5doiSubjects--Topical Terms:
583857
Bioinformatics.
LC Class. No.: QH324.2-324.25
Dewey Class. No.: 570.285
Hidden Treasures in Contemporary RNA Sequencing
LDR
:03412nam a22004095i 4500
001
1011904
003
DE-He213
005
20200701155807.0
007
cr nn 008mamaa
008
210106s2019 gw | s |||| 0|eng d
020
$a
9783030139735
$9
978-3-030-13973-5
024
7
$a
10.1007/978-3-030-13973-5
$2
doi
035
$a
978-3-030-13973-5
050
4
$a
QH324.2-324.25
072
7
$a
PSA
$2
bicssc
072
7
$a
COM014000
$2
bisacsh
072
7
$a
PSA
$2
thema
072
7
$a
UB
$2
thema
082
0 4
$a
570.285
$2
23
100
1
$a
Mangul, Serghei.
$e
author.
$4
aut
$4
http://id.loc.gov/vocabulary/relators/aut
$3
1306152
245
1 0
$a
Hidden Treasures in Contemporary RNA Sequencing
$h
[electronic resource] /
$c
by Serghei Mangul, Harry Taegyun Yang, Eleazar Eskin, Noah Zaitlen.
250
$a
1st ed. 2019.
264
1
$a
Cham :
$b
Springer International Publishing :
$b
Imprint: Springer,
$c
2019.
300
$a
V, 93 p. 49 illus., 48 illus. in color.
$b
online resource.
336
$a
text
$b
txt
$2
rdacontent
337
$a
computer
$b
c
$2
rdamedia
338
$a
online resource
$b
cr
$2
rdacarrier
347
$a
text file
$b
PDF
$2
rda
490
1
$a
SpringerBriefs in Computer Science,
$x
2191-5768
505
0
$a
Abstract -- Main Text -- Acknowledgement -- Disclosure -- References.
520
$a
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.
650
0
$a
Bioinformatics.
$3
583857
650
0
$a
Genetics.
$3
578972
650
1 4
$a
Computational Biology/Bioinformatics.
$3
677363
650
2 4
$a
Genetics and Genomics.
$3
1229010
700
1
$a
Yang, Harry Taegyun.
$e
author.
$4
aut
$4
http://id.loc.gov/vocabulary/relators/aut
$3
1306153
700
1
$a
Eskin, Eleazar.
$4
aut
$4
http://id.loc.gov/vocabulary/relators/aut
$3
674625
700
1
$a
Zaitlen, Noah.
$e
author.
$4
aut
$4
http://id.loc.gov/vocabulary/relators/aut
$3
1306154
710
2
$a
SpringerLink (Online service)
$3
593884
773
0
$t
Springer Nature eBook
776
0 8
$i
Printed edition:
$z
9783030139728
776
0 8
$i
Printed edition:
$z
9783030139742
830
0
$a
SpringerBriefs in Computer Science,
$x
2191-5768
$3
1255334
856
4 0
$u
https://doi.org/10.1007/978-3-030-13973-5
912
$a
ZDB-2-SCS
912
$a
ZDB-2-SXCS
950
$a
Computer Science (SpringerNature-11645)
950
$a
Computer Science (R0) (SpringerNature-43710)
based on 0 review(s)
Multimedia
Reviews
Add a review
and share your thoughts with other readers
Export
pickup library
Processing
...
Change password
Login