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Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells

Y. Chu, T. Wang, D. Dodd, Y. Xie, B. A. Janowski, D. R. Corey
<span title="2015-03-26">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
This RNA self-circularization approach to RNA sequencing (RC-Seq) allows data to be obtained using small amounts of input RNA that cannot be sequenced by standard methods.  ...  Using our method, we generated CLIP-Seq libraries from nuclear RNA that had been UV-crosslinked and immunoprecipitated with anti-Argonaute 2 (Ago2) antibody.  ...  Five different groups of reads, 20 nt, 40 nt, 60 nt, 80 nt and 100 nt, were used in the simulation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv213">doi:10.1093/nar/gkv213</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25813040">pmid:25813040</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4477644/">pmcid:PMC4477644</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3myki5pxorcxxnjznjqtnhmgfe">fatcat:3myki5pxorcxxnjznjqtnhmgfe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219183504/http://pdfs.semanticscholar.org/1930/fc65aafc65c65e22d3612bd2bfc184b6a027.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/19/30/1930fc65aafc65c65e22d3612bd2bfc184b6a027.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv213"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477644" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq) Data

Yuxiang Tan, Yann Tambouret, Stefano Monti
<span title="">2015</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
Although a few simulated fusion datasets from RNA Sequencing (RNA-Seq) are available, they are of limited sample size.  ...  SimFuse utilizes real sequencing data as the fusions' background to closely approximate the distribution of reads from a real sequencing library and uses a reference genome as the template from which to  ...  This is a unique feature that no other simulated RNA-Seq fusion dataset provides.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2015/780519">doi:10.1155/2015/780519</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26839886">pmid:26839886</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4709598/">pmcid:PMC4709598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/or25l33hgrcjhg6bcvpgr6hbay">fatcat:or25l33hgrcjhg6bcvpgr6hbay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221002319/http://pdfs.semanticscholar.org/2a6c/91b77289f6ea28f35b42cdbc66f1fb7ef246.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2a/6c/2a6c91b77289f6ea28f35b42cdbc66f1fb7ef246.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2015/780519"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709598" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

Xiao Xu, Yuanhao Zhang, Jennie Williams, Eric Antoniou, W McCombie, Song Wu, Wei Zhu, Nicholas O Davidson, Paula Denoya, Ellen Li
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The DESeq and baySeq algorithms (RNA-Seq) and the SAM and eBayes algorithms (microarray) achieved the highest cross-platform overlap rate in DEG results from both experimental and simulated datasets.  ...  Conclusions: These results suggest that RNA-Seq has advantages over microarray in identification of DEGs with the most consistent results generated from DESeq and SAM methods.  ...  Acknowledgements The authors would like to thank Molly Hammel from Cold Spring Harbor Laboratory for her valuable suggestions in the RNA-Seq data analysis process.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s9-s1">doi:10.1186/1471-2105-14-s9-s1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23902433">pmid:23902433</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3697991/">pmcid:PMC3697991</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6dhbrbbb2ndkbc7vcgzjmhevoa">fatcat:6dhbrbbb2ndkbc7vcgzjmhevoa</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3697991/PMC3697991-1471-2105-14-S9-S1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b5/5a/b55a69fc5ccc514018524bb7d33d6f2218c99311.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s9-s1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697991" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies

Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D'Angelo, Antonina Sidoti
<span title="2021-06-16">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a3wauupnbbdj7hbo62upc6grdq" style="color: black;">Neural computing &amp; applications (Print)</a> </i> &nbsp;
The chosen tools were assessed on empirical human DNA- and RNA-Seq data, as well as on simulated datasets in human and mouse, evaluating a set of parameters previously not considered in such kind of benchmarks  ...  For Ion Torrent single-end RNA-Seq samples, the most suitable aligners were CLC and BWA-MEM, which reached the best results in terms of efficiency, accuracy, duplication rate, saturation profile and running  ...  (2013) 1535 TOPHAT2 2.1.1 RNA 50 51 (50 bp), 60 (150 bp), 62 (200 bp)* FM index It aligns RNA-Seq reads to mammalian- sized genomes using the ultra-high- throughput short read aligner  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00521-021-06188-z">doi:10.1007/s00521-021-06188-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34155424">pmid:34155424</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8208613/">pmcid:PMC8208613</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/podomi2hezbedowkjesolx7ov4">fatcat:podomi2hezbedowkjesolx7ov4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718084743/https://link.springer.com/content/pdf/10.1007/s00521-021-06188-z.pdf?error=cookies_not_supported&amp;code=7f55fd7b-6afc-4687-b5fc-ebb581895323" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/99/6f/996f1ee7f7f4d619e331f4f3b18d131b81760978.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00521-021-06188-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208613" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome

Steven W. Wingett, Simon Andrews, Peter Fraser, Jörg Morf
<span title="2020-01-28">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a577b42d4nfhddl7kurxnuyzem" style="color: black;">Scientific Data</a> </i> &nbsp;
We have previously developed and described a method for measuring RNA co-locations within cells, called Proximity RNA-seq, which promises insights into RNA expression, processing, storage and translation  ...  Here, we describe transcriptome-wide proximity RNA-seq datasets obtained from human neuroblastoma SH-SY5Y cell nuclei.  ...  We recommend using GSL 2.4.Fig. 3 Pairwise Spearman rank correlation coefficients between different Proximity RNA-seq libraries.Correlations between different Proximity RNA-seq datasets using the number  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41597-020-0372-3">doi:10.1038/s41597-020-0372-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31992717">pmid:31992717</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6987088/">pmcid:PMC6987088</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3yw3mboypfevzmfxqw2q7croea">fatcat:3yw3mboypfevzmfxqw2q7croea</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200402124333/https://www.repository.cam.ac.uk/bitstream/handle/1810/303900/RNA%20proximity%20sequencing%20data%20and%20analysis%20pipeline%20from%20a%20human%20neuroblastoma%20nuclear%20transcriptome.pdf;jsessionid=42170ABAB87B91E974DBF04A2EC359C1?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ee/71/ee716e656d34bc5c55c413fd33f792b77688ce6b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41597-020-0372-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6987088" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data

Qian Zhou, Xiaoquan Su, Gongchao Jing, Songlin Chen, Kang Ning
<span title="2018-02-14">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
RNA-Seq has become one of the most widely used applications based on next-generation sequencing technology.  ...  Conclusions: We present here a tool, RNA-QC-Chain, which can be used to comprehensively resolve the quality control processes of RNA-Seq data effectively and efficiently.  ...  The "strand specificity" monitors the template strand used in the sequencing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-018-4503-6">doi:10.1186/s12864-018-4503-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29444661">pmid:29444661</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5813327/">pmcid:PMC5813327</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o3yatxqhszefraus3uc3an5hjy">fatcat:o3yatxqhszefraus3uc3an5hjy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719153231/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-018-4503-6?site=bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bc/f2/bcf2e29b4cee47bad7b34bddee0750a680650943.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-018-4503-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813327" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

Yuan Gao, Jinfeng Wang, Fangqing Zhao
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
By applying CIRI to ENCODE RNA-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circRNAs as well as fragments specific to them in the human transcriptome  ...  Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals.  ...  CIRI is fast for small data sets (for example, <5 Gb RNA-seq data) and spends less than half an hour on a 7.5G SAM file using high stringency.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-014-0571-3">doi:10.1186/s13059-014-0571-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25583365">pmid:25583365</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4316645/">pmcid:PMC4316645</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zh2aibr7pfetzj6v3w6vxb7tiq">fatcat:zh2aibr7pfetzj6v3w6vxb7tiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171008215418/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/0e6/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMDU5LTAxNC0wNTcxLTMucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ee/55/ee557a7f8fbba89deeaa8795bacdaed5a2da483f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-014-0571-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316645" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CSEQ-SIMULATOR: A DATA SIMULATOR FOR CLIP-SEQ EXPERIMENTS

WANJA KASSUHN, UWE OHLER, PHILIPP DREWE
<span title="2015-11-18">2015</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2016 </i> &nbsp;
In this work, we also show how Cseq-Simulator can be used to perform a comparison of steps of typical CLIP-Seq analysis pipelines, such as the read alignment or the peak calling.  ...  CLIP-Seq protocols such as PAR-CLIP, HITS-CLIP or iCLIP allow a genome-wide analysis of protein-RNA interactions. For the processing of the resulting short read data, various tools are utilized.  ...  We used these reads as templates to simulate three different groups of reads: Reads with T-C conversions, deletions or truncations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814749411_0040">doi:10.1142/9789814749411_0040</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gxf6xpa62fh23fvhz4jxfk63bu">fatcat:gxf6xpa62fh23fvhz4jxfk63bu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170317093541/http://psb.stanford.edu/psb-online/proceedings/psb16/kassuhn.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/9b/ef9b820c77a64303c2ecb18771c2ac14da206b63.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789814749411_0040"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer

Lisle E. Mose, Sara R. Selitsky, Lisa M. Bixby, David L. Marron, Michael D. Iglesia, Jonathan S. Serody, Charles M. Perou, Benjamin G. Vincent, Joel S. Parker
<span title="2016-08-24">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
This method captures expressed BCR loci from a standard RNA-seq assay.  ...  Additionally, there are many existing datasets where short-read RNA sequencing data are available but PCR amplified BCR data are not.  ...  V'DJer showed superior performance to this method in the context of bulk RNA-seq data including reads from a diverse underlying BCR repertoire.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw526">doi:10.1093/bioinformatics/btw526</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27559159">pmid:27559159</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5167060/">pmcid:PMC5167060</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iozrihxdbzh65gmrkt5z4yxfou">fatcat:iozrihxdbzh65gmrkt5z4yxfou</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307211551/http://pdfs.semanticscholar.org/e6df/a004448fa6770918a0fb4ed6c7f0af34a1a1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/df/e6dfa004448fa6770918a0fb4ed6c7f0af34a1a1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btw526"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167060" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Suitability of different mapping algorithms for genome-wide polymorphism scans with Pool-Seq data [article]

Robert Kofler, Anna Maria Langmueller, Pierre Nouhaud, Kathrin Anna Otte, Christian Schloetterer
<span title="2016-05-11">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools leading to characteristic false positives in genome-wide scans.  ...  The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and wide-spread use of this method for many research questions, ranging from unravelling the genetic  ...  For gsnap we used sam as output format (-A sam). Only 13 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/052845">doi:10.1101/052845</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ppdy2c4euva6jiogpg732buou4">fatcat:ppdy2c4euva6jiogpg732buou4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501092527/https://www.biorxiv.org/content/biorxiv/early/2016/05/11/052845.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dd/59/dd59b97a1c1793da48e0e8735a34146989ecfa6c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/052845"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Evaluation of tools for long read RNA-seq splice-aware alignment [article]

Kresimir Krizanovic, Amina Echchiki, Julien Roux, Mile Sikic
<span title="2017-04-11">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This tool can be used to compare the alignment of simulated reads to their genomic origin, or to compare the alignment of real reads to a set of annotated transcripts.  ...  A tool was developed for evaluating RNA-seq alignment results.  ...  RNA-seq reads.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/126656">doi:10.1101/126656</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3cgvqix5onb23bltxomc45b2ce">fatcat:3cgvqix5onb23bltxomc45b2ce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503102231/https://www.biorxiv.org/content/biorxiv/early/2017/04/11/126656.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/00/d2/00d274f162136fe0b3efb0d96ec021e8f8963fbc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/126656"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Suitability of Different Mapping Algorithms for Genome-wide Polymorphism Scans with Pool-Seq Data

R. Kofler, A. M. Langmuller, P. Nouhaud, K. A. Otte, C. Schlotterer
<span title="2016-09-09">2016</span> <i title="Genetics Society of America"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lmrbfynd2rbtzo6uhqthfvnwci" style="color: black;">G3: Genes, Genomes, Genetics</a> </i> &nbsp;
Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools leading to characteristic false positives in genome-wide scans.  ...  The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and wide-spread use of this method for many research questions, ranging from unravelling the genetic  ...  For gsnap we used sam as output format (-A sam).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1534/g3.116.034488">doi:10.1534/g3.116.034488</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27613752">pmid:27613752</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5100849/">pmcid:PMC5100849</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vqeuyzkeprgjxeakzm2vbjh45q">fatcat:vqeuyzkeprgjxeakzm2vbjh45q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309030149/http://pdfs.semanticscholar.org/f280/c65c18bc9f27ad2f51196edf26e89b2ec3d5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f2/80/f280c65c18bc9f27ad2f51196edf26e89b2ec3d5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1534/g3.116.034488"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100849" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Study ofTP53RNA Splicing Illustrates Pitfalls of RNA-seq Methodology

Sunali Mehta, Peter Tsai, Annette Lasham, Hamish Campbell, Roger Reddel, Antony Braithwaite, Cristin Print
<span title="2016-10-20">2016</span> <i title="American Association for Cancer Research (AACR)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/czhppgb4znaghaxcyto6oc7jhe" style="color: black;">Cancer Research</a> </i> &nbsp;
Using RNA-seq simulation analysis, we determined why RNA-seq is unable to detect less abundant TP53 transcripts and discuss the implications of these findings for the general interpretation of RNA-seq  ...  In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The  ...  We would also like to thank New Zealand Genomics Limited for preparing the RNA-seq libraries for the nine cell lines and Jane Noble for authenticating the cell lines. Grant Support  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1158/0008-5472.can-16-1624">doi:10.1158/0008-5472.can-16-1624</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27913434">pmid:27913434</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ralgng2v7bevxdix4c56vqxbta">fatcat:ralgng2v7bevxdix4c56vqxbta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430195334/http://cancerres.aacrjournals.org/content/canres/76/24/7151.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/13/ae13df58a24003c2ed3a16c3c1aa4ccffa722c02.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1158/0008-5472.can-16-1624"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Trans-NanoSim characterizes and simulates nanopore RNA-seq data [article]

Saber Hafezqorani, Chen Yang, Ka Ming Nip, Rene L Warren, Inanc Birol
<span title="2019-10-10">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We introduce Trans-NanoSim, the first tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-seq data.  ...  Through benchmarking on sets of nanopore reads from human and mouse reference transcriptomes, we show the robustness of Trans-NanoSim in capturing the characteristics of nanopore cDNA and direct RNA reads  ...  As the first ONT RNA-seq read simulator, Trans-NanoSim will offer important resources to the community.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/800110">doi:10.1101/800110</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3py5sks4ercczmygc735z3pr64">fatcat:3py5sks4ercczmygc735z3pr64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711035111/https://www.biorxiv.org/content/biorxiv/early/2019/10/10/800110.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/24/4e/244edaa945ebed0fd54443db035db1a7da9e6855.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/800110"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A platform independent RNA-Seq protocol for the detection of transcriptome complexity

Claudia Calabrese, Marina Mangiulli, Caterina Manzari, Anna Paluscio, Mariano Caratozzolo, Flaviana Marzano, Ivana Kurelac, Anna D'Erchia, Domenica D'Elia, Flavio Licciulli, Sabino Liuni, Ernesto Picardi (+6 others)
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
In this frame, one of the key aims of high throughput transcriptome sequencing is the detection of all RNA species present in the cell and the first crucial step for RNA-seq users is represented by the  ...  Indeed, most transcripts are the result of antisense, overlapping and non-coding RNA expression.  ...  Indeed, strand-specificity information is useful to correctly map reads that do not contain polyA tails or splice junctions and represent a challenge in the annotation step of RNA-seq reads.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-855">doi:10.1186/1471-2164-14-855</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24308330">pmid:24308330</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4046740/">pmcid:PMC4046740</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ahtd2mrpivesriceln6ykv6rvy">fatcat:ahtd2mrpivesriceln6ykv6rvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830104852/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-14-855?site=http://bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/49/f1/49f192fd6de0693f3a3d7f383e19c49719bdb7f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-855"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046740" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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