ライフサイエンスコーパス: paired-end

1 as for incomplete overlap among reads (e.g. paired-end).

2 y for any level up to, and including, 100 bp paired-end.

3 nstructs potential splicing paths connecting paired ends.

4 We used paired-end 101 bp reads and trimmed them to simulate dif

5 We obtained ~219 million paired-end 125-bp Illumina reads from five time-courses

6 on of non-trivial signatures from discordant paired-end alignments, split-reads and read depth inform

7 Our data set is produced using the paired-end analysis of transcription start sites (PEAT)

8 Paired-end and coverage information is used to predict S

9 ear-complete genomes, assembled de novo with paired-end and long-mate-pair (8 kb) libraries were firs

10 cing detection is unquestionably improved by paired-end and longer reads.

11 This workflow enables the analysis of both paired-end and single-end ChIP-Seq reads, with or withou

12 Not only did a paired-end approach provide a greater dynamic range in c

13 ified threshold, and supplements that with a paired-end approach to identify larger variants that are

14 higher sensitivity and specificity than the paired-end approach when the inner distance between read

15 current bioinformatics tools heavily rely on paired-end approaches and overlook the importance of rea

16 urately estimate the PCR duplication rate on paired-end as well as single-end read datasets which con

17 le error-corrected sequences; it can process paired-end as well as single-end reads.

18 Users submit a bedpe (paired-end BED format) file containing the locations and

19 (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE).

20 transcript connectivity information through paired-end cDNA sequencing.

21 computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1

22 We generated 101 bps paired-end ChIP-seq data for many transcription factors

23 relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference g

24 1 A resolution crystal structure of the Mos1 paired-end complex containing the pre-cleaved left IR se

25 hitecture of this pre-second strand cleavage paired-end complex supports our proposal that second str

26 izes all steps during NHEJ within the stable paired-end complex to limit end processing and associate

27 When paired ends could not be merged, a congruent strategy in

28 The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system

29 em correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depl

30 es and duplicates, generates strand-specific paired-end data and is highly reproducible.

31 In addition, paired-end data were assembled and analyzed using a comm

32 the commercial software was used to assemble paired-end data, and resolved assemblies were used to pe

33 This was performed on an RNA-Seq paired-end dataset derived from alcohol-exposed neural f

34 can detect fusion events in both single- and paired-end datasets from either RNA-Seq or gDNA-Seq stud

35 We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and co

36 result in a loss of sensitivity compared to paired-end datasets without size-selection.

37 Paired-end deep sequencing identified more than 200 de n

38 Here, we used paired-end deep sequencing of mRNA to identify genes tha

39 extension (SHAPE) chemistry with multiplexed paired-end deep sequencing of primer extension products.

40 After PCR, we applied paired-end deep sequencing to read the two barcodes and

41 sis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment

42 porates various cues from read alignment and paired-end distance distribution, as well as a sequence

43 files derived from next-generation (nextGen) paired-end DNA and cDNA sequencing as input, call on sev

44 enomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And

45 e block organization of a cancer genome from paired-end DNA sequencing data.

46 ei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleoso

47 Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-l

48 s DNA and adds adapters ('tagmentation') for paired-end DNA sequencing.

49 otein-DNA complexes into the supernatant for paired-end DNA sequencing.

50 Through novel statistical modeling of paired-end DNA-sequencing data using blood-derived DNA f

51 ome sequence as input and outputs artificial paired-end FASTQ files containing Phred quality scores.

52 es be ribodepleted and sequenced in a 100 bp paired end format with a minimum of 40 million reads per

53 RNA was extracted and sequenced (75 bp paired-end) from bronchial lymph nodes.

54 can produce tens of millions of reads, often paired-end, from transcripts or genomes.

55 erization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly

56 SV) that detects SVs with high accuracy from paired-end high-throughput genomic sequencing data and p

57 By analyzing paired-end high-throughput sequence data from polytene l

58 ution that permits users to merge and filter paired end illumina reads.

59 a were assembled into c. 22,000 isotigs, and paired-end Illumina reads for phosphorus-starved (P-) an

60 We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic c

61 Paired-end Illumina sequencing of ssDNA revealed interge

62 nd is compatible with standard and multiplex paired-end Illumina sequencing.

63 ur rounds of antigen selections by multiplex paired-end Illumina sequencing.

64 bacterial 16S ribosomal RNA was subjected to paired-end Illumina sequencing.

65 ion PCR, and interrogated by high-throughput paired-end Illumina sequencing.

66 ble to efficiently use both multi-splice and paired-end information to the fullest extent.

67 raph, weighted by a bin-packing strategy and paired-end information.

68 llite loci from short sequence reads without paired-end information.

69 encing data, especially when they exceed the paired-end insert size.

70 without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of in

71 generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of

72 The use of paired-end libraries with a fragment size shorter than t

73 se they use a peak-calling step that ignores paired-end linkage information.

74 Given paired-end mapped reads, and a candidate high-copy regio

75 Paired end mapping of chromosomal fragments has been use

76 These paired-end mapping patterns reveal a greater diversity a

77 d been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR.

78 onal methods can be adapted to identify most paired-end mapping patterns.

79 orithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genom

80 ed to call short insertion variants based on paired-end mapping.

81 Using paired-end massively parallel sequencing of cDNA (RNA-se

82 n is choosing one based on read overlaps and paired-end (mate-pair) reads.

83 -source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chr

84 We sequenced the herring genome generating paired-end, mate-pair, linked and long reads.

85 line performs sample demultiplexing, overlap paired-end merging, alignment, MIP-arm trimming, variant

86 as well as next-generation sequencing with "paired-end" methods, has enabled a whole-genome analysis

87 gestion of chromatin, can be sequenced using paired-end mode next-generation technology.

88 st tumors, SnowShoes-FTD was used to analyze paired-end mRNA-Seq data from a panel of estrogen recept

89 developed for fusion transcript detection in paired-end mRNA-Seq data, employs multiple steps of fals

90 Here, we use paired-end next-generation RNA sequencing (RNA-seq) to c

91 ent to the nucleotide level within single or paired-end NGS data.

92 g de novo assembly of massive short (90 bp), paired-end or single-end reads.

93 It aligns paired-end (PE) reads and preassembled contigs or scaffo

94 Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage

95 ted it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom

96 enetic relationships) or the availability of paired end read libraries.

97 enomes, we evaluated library size selection, paired end read strategy, and sequencing depth.

98 The RNA-seq paired-end read (PER) protocol samples transcript fragme

99 _DETECTION is able to detect DDs purely from paired-end read alignments.

100 n protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and prese

101 It provides a complementary paired-end read homology search tool to HMMER.

102 Second, we present a sequence-to-PRG paired-end read mapping algorithm that enables accurate

103 ce coverage overviews, variant highlighting, paired-end read mark-up, GFF3-based feature tracks and p

104 taneously uses split read signal, discordant paired-end read signal, read depth signal and the fragme

105 analyzed using a combination of single read, paired-end read, and long read RNA sequencing.

106 should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 fo

107 blicly available data, we test whether short-paired end reads can achieve more robust expression esti

108 l sequence of insertion events from Illumina paired end reads.

109 e, and is able to profile 1 million Illumina paired-end reads against over 40 K genomes on 64 machine

110 upports multiplexed primer pools, single- or paired-end reads and emerging technologies that use sing

111 Our tool, BRAT, supports single and paired-end reads and handles input files containing read

112 BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing p

113 ation data analysis that supports single and paired-end reads and includes a tool for estimation of m

114 na NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be gene

115 Using 100 bp paired-end reads and minimal manual curation, we produce

116 are scheme for paired-end reads) for merging paired-end reads and provides users the option to qualit

117 to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads.

118 a platform, merging and quality filtering of paired-end reads are essential first steps in data analy

119 uring this stage, contigs assembled from the paired-end reads are merged into bigger chains called sc

120 t Program), which can align both single- and paired-end reads as short as 14 nt and of arbitrarily lo

121 rm one or multiple processing steps, such as paired-end reads assembly, chimera filtering, Operationa

122 sitioning analyses, or the ability to subset paired-end reads by groups of insert size that can conta

123 inversion breakpoints using next-generation paired-end reads derived from D. melanogaster isofemale

124 from 3'-end RNA-Seq data by exploiting both paired-end reads for gene isoform identification and qua

125 end the length of short reads by overlapping paired-end reads from fragment libraries that are suffic

126 n in C++, the application accepts single and paired-end reads in FASTQ and FASTA formats and decompre

127 Our method transforms large numbers of paired-end reads into a much smaller number of longer 's

128 GangSTR extracts information from paired-end reads into a unified model to estimate maximu

129 cing technology, using high-quality Illumina paired-end reads mapped onto the long reads.

130 evel expression analysis should prefer short paired-end reads over a longer single-end strategy.

131 ng to the human genome 550 million 2 x 76 bp paired-end reads per hour on a modest 12-core server, wh

132 t longer reads are more informative and that paired-end reads produce better results than single-end

133 transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotat

134 ility by generating >30,000 Escherichia coli paired-end reads separated by 1, 2, or 3 kb using in sit

135 the African puff adder Bitis arietans using paired-end reads sequenced on Illumina's MiSeq platform.

136 Importantly, the paired-end reads that are properly aligned to the bovine

137 entional de novo assembler and alignments of paired-end reads to assemble cyclic sequences likely to

138 We present a method for using paired-end reads to find fusion transcripts without requ

139 both the transcript and gene levels, 2 x 40 paired-end reads unequivocally provide expression estima

140 tal, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yi

141 Short paired-end reads will also give reasonably robust expres

142 s, which may eventually generate billions of paired-end reads with a high sequencing cost.

143 Other features include automatic support for paired-end reads with arbitrary insert sizes.

144 FiT invokes CASPER (context-aware scheme for paired-end reads) for merging paired-end reads and provi

145 mate pair orientation and insert length (for paired-end reads), sequencing coverage, read alignment a

146 nstruction by incorporating information from paired-end reads, and demonstrate its utility on simulat

147 e genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both.

148 os: it is able to handle both single-end and paired-end reads, it does not rely on the presence of ca

149 m that automatically generates bidirectional paired-end reads, pinpointing the position of modified n

150 the following: whole-genome sequencing using paired-end reads, single-nucleotide polymorphism (SNP) g

151 e using massively parallel pyrosequencing of paired-end reads, that UCYN-A has a photofermentative me

152 6-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on

153 Tedna uses Illumina paired-end reads, the most widely used sequencing techno

154 When using short 100 bp paired-end reads, we found that using mixtures of insert

155 man WGS sequencer run-over 500 million 150nt paired-end reads-in less than 15 minutes.

156 er long reads (longer than 100 bp) or joined paired-end reads.

157 on an Illumina Miseq, generating 20 million paired-end reads.

158 rom whole genome resequencing datasets using paired-end reads.

159 res favourably to that obtained from regular paired-end reads.

160 on sequencing platform to generate 100 bases paired-end reads.

161 put data, including both single-stranded and paired-end reads.

162 nts using comparative genome information and paired-end reads.

163 verage) assembled from short Illumina 150 bp paired-end reads.

164 plit-read mapping within focal regions using paired-end reads.

165 ated RNA-Seq datasets, which contained 75 nt paired-end reads.

166 s for soft-masked alignments and overlapping paired-end reads.

167 rect for sequencing errors using overlapping paired-end reads.

168 d RNA-sequencing samples using long (126-bp) paired-end reads.

169 ibraries on both platforms using single- and paired-end reads.

170 gerprint (as k-mers) profiles of the RNA-Seq paired-end reads.

171 from both exon-exon junctions and discordant paired-end reads.

172 named Short-Pair that is designed for short paired-end reads.

173 costs with increasing read-lengths and true paired-end reads.

174 antly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Ass

175 -throughput sequencing (total of 354,505,167 paired-ended reads).

176 We design an efficient algorithm, called Paired-end Reconstruction of Genome Organization (PREGO)

177 Here, we used paired end RNA sequencing (RNA-seq) to explore the trans

178 Paired-end RNA sequencing (RNA-Seq) was used to explore

179 Here, we use strand-specific paired-end RNA sequencing (ssRNA-seq) data from 376 canc

180 Analyses of 126 paired-end RNA sequencing libraries, spanning nine time

181 Paired-end RNA sequencing on blood lymphocytes of SCAF4-

182 Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level

183 chondrial and nuclear transcriptomes by deep paired-end RNA sequencing.

184 ective of this study was to compare parallel paired-end RNA-Seq and microarray data generated on 5-az

185 detection algorithms have been developed for paired-end RNA-seq data but their performance has not be

186 Using paired-end RNA-Seq data from breast cancer cell lines, F

187 expressed SNVs (eSNVs) from non-directional paired-end RNA-Seq data.

188 vel fusion detection tool, FusionQ, based on paired-end RNA-Seq data.

189 thod to quantify exon inclusion levels using paired-end RNA-seq data.

190 e by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality

191 tion of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of altern

192 Performing paired-end RNA-Seq of the breast cancer cell line MCF-7

193 We applied a tailored paired-end RNA-seq protocol to specifically probe the po

194 use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop

195 transcripts from transcriptional analysis of paired-end RNA-seq.

196 Using a paired-end RNA-sequencing approach, we report the discov

197 e-transposon fusions in standard single- and paired-end RNA-sequencing data.

198 Using paired-end RNAseq method, we performed a transcriptome a

199 ements, such as viral genome integration, in paired-end sequence data.

200 sassembly errors and their breakpoints using paired-end sequence reads and optical mapping data.

201 A single "lane" of paired-end sequences (2 x 76 bp) provides a good synteni

202 We analysed 22.9 Gb of paired-end sequences and identified and scored >3000 hig

203 ere we produce a draft genome using 181-fold paired-end sequences assisted by fivefold BAC-to-BAC seq

204 y, it is possible to reliably produce 300 bp paired-end sequences for RNA expression analysis.

205 High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides str

206 Most approaches that use discordant paired-end sequences ignore non-trivial signatures prese

207 ses of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were gen

208 Paired-end sequences were assembled and used for structu

209 ic shotgun sequencing, generating 17 billion paired-end sequences, which were processed using HUMAnN2

210 ng of random-primed products and (2) 2-sided paired-end sequences.

211 ranscriptome on Illumina GAIIX platform with paired end sequencing for obtaining short reads.

212 Massively parallel paired-end sequencing allowed identification of a cytoge

213 Paired-end sequencing allows circumventing the shortness

214 Using complementary experiments by capture/paired-end sequencing and FISH experiments, various type

215 d that the additional benefits obtained from paired-end sequencing are not worth the additional cost.

216 Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance s

217 lasmid vector that can then be amplified and paired-end sequencing by next-generation sequencing (NGS

218 Paired-end sequencing conflicts reveal differences in re

219 data, such as single-end sequencing data or paired-end sequencing data can accommodate to detect SV.

220 We apply the presented techniques to paired-end sequencing data from pancreatic tumors and co

221 ge, iMARGI-Docker, is provided to decode the paired-end sequencing data into caRNA-DNA interactions.

222 pe novel Numt insertions using whole genome, paired-end sequencing data.

223 method versus those that were "observed" in paired-end sequencing data.

224 th high precision from standard, short-read, paired-end sequencing datasets.

225 Paired-end sequencing is a common approach for identifyi

226 An alternative paired-end sequencing method using interstrand DNA photo

227 iciency, a convergent fusion vector to allow paired-end sequencing of interactors, and the use of pro

228 recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to

229 xes in Saccharomyces cerevisiae, obtained by paired-end sequencing of micrococcal nuclease-resistant

230 Our genome-wide paired-end sequencing of nucleosomal DNA reveals that th

231 We have used paired-end sequencing of yeast nucleosomal DNA to obtain

232 We have shown previously, using paired-end sequencing of yeast nucleosomes, that major c

233 s from circulating memory B cells with 2x250 paired-end sequencing on the Illumina MiSeq platform.

234 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumin

235 riation using next-generation, short-insert, paired-end sequencing reads.

236 Paired-end sequencing revealed that single-end data unde

237 Here we describe a paired-end sequencing strategy, which enables more robus

238 Although paired-end sequencing technologies are commonly used for

239 llination and pollination stages by Illumina paired-end sequencing technology to de novo sequence six

240 nomic fusion events, we applied whole-genome paired-end sequencing to identify structural alterations

241 inverse PCR generates a jumping library for paired-end sequencing with 101-base reads.

242 lls from 3 patients for whole transcriptome, paired-end sequencing with an average depth of 112 milli

243 Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method.

244 -seq (Multiplexed *OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary str

245 amplicons >500 bp using Illumina short read paired-end sequencing.

246 on library in preparation for Illumina Miseq paired-end sequencing.

247 based on micrococcal nuclease digestion and paired-end sequencing.

248 ing the genome by 112.6-fold was obtained by paired-end sequencing.

249 hen perform affinity purification of TFs and paired-end sequencing.

250 -Seq data combined with either single-end or paired-end sequencing.

251 on of chromothripsis, which was confirmed by paired-end sequencing.

252 re targeted and sampled with 454 or Illumina paired-end sequencing.

253 -CGH and may be interpreted as insertions by paired-end sequencing.

254 benefitting from the current availability of paired-end sequencing.

255 erted into a sequencing library suitable for paired-end sequencing.

256 ch are converted to a sequencing library for paired-end sequencing.

257 by gentle shearing, ChIP, biotin capture and paired-end sequencing.

258 20-bp barcode is constructed, and decoded by paired-end sequencing.

259 -generation library preparation for Illumina paired-end sequencing.

260 e deletions and medium-sized insertions from paired-end short reads.

261 Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone

262 ves as the read length increases with 100 bp paired-end showing the best performance.

263 ct large SVs, while it leverages read depth, paired-end signals and local assembly to detect small SV

264 However, paired-end strategies do not accurately predict precise

265 ymerase II chromatin interaction analysis by paired-end tag (ChIA-PET) reveals that rhythmic BMAL1 ta

266 Based on chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing data, we used CRISP

267 RG), using chromatin interaction analysis by paired-end tag (ChIA-PET).

268 We generated single-end tag (SET) and paired-end tag (PET) ChIP-Seq data for sigma(7)(0) facto

269 A chromatin interaction analysis followed by paired-end tag sequencing (ChIA-PET) data linked EBV enh

270 al Chromatin Interaction Analysis by in-situ Paired-End Tag Sequencing (ChIA-PET) data, we confirmed

271 878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeti

272 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a method for the

273 Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a popular assay

274 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a robust method

275 Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established m

276 erformed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subu

277 n advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to compreh

278 We used chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to comprehensively

279 ops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene

280 , chromatin interaction analysis followed by paired-end tag sequencing (ChIA-PET), and genome-wide cl

281 eractions (chromatin interaction analysis by paired-end tag sequencing and HiChIP) have yielded treme

282 resolution chromatin interaction analysis by paired-end tag sequencing of P300, we observed agonist-i

283 g 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hyb

284 s (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET)(3), have revealed t

285 hrough a chromatin interaction analysis with paired-end tagging approach using an antibody that prima

286 e original ChIA-PET protocol generates short paired-end tags (2 x 20 base pairs (bp)) to detect two g

287 3D contacts are counted from paired-end tags (PETs) from the human genome and are nor

288 ng-read ChIA-PET, in which the length of the paired-end tags is increased (up to 2 x 250 bp).

289 In particular, a paired-end tetraloop (no hanging TR) is stable in (CAG)n

290 Using the paired-end transcriptome sequencing approach, we observe

291 Here we used paired-end transcriptome sequencing to explore the lands

292 Here we used paired-end transcriptome sequencing to screen ETS rearra

293 Using paired-end transcriptome sequencing, we identified recur

294 We demonstrated paired-end TSS analysis to be a powerful method to uncov

295 A extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics

296 nger read lengths were acheivable by merging paired ends when the sequencing library was size-selecte

297 verified Hepatitis B Virus chimeras within a paired-end Whole Genome Sequencing hepatocellular carcin

298 Paired-end whole transcriptome sequencing provides evide

299 Paired-end whole-genome NGS was performed on the Illumin

300 ng non-reference TE insertions from Illumina paired-end whole-genome sequencing data.