How to store and visualize RNA-seq data

Dec 04, 2013

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How to store and visualize RNA-seq data

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RNA-Seq

RNA-Seq. An alternative to microarray. Grow cells or isolate tissue (brain, liver, muscle) Isolate total RNA Isolate mRNA from total RNA (poly A+ select) Fragment RNA Make and amplify cDNA Sequence the ends of the cDNA Map the sequences to the human genome

353 views • 17 slides

RNA-Seq and transcriptome analysis

RNA-Seq and transcriptome analysis. Radhika S. Khetani, Ph.D. Technical Lead, User Support & Training, HPCBio Roy J. Carver Biotechnology Center. RNA-Seq or T ranscriptome Sequencing Transcriptome

1.38k views • 67 slides

Expression A nalysis of RNA - seq Data

Expression A nalysis of RNA - seq Data. Manuel Corpas Plant and Animal Genomes Project Leader m anuel.corpas @ tgac.ac.uk. Generation of Sequence. Mapping Reads. Identification of splice junctions. Assembly of Transcripts. Statistical Analysis

448 views • 20 slides

RNA- seq Analysis

Please DO NOT switch on your computers – yet. RNA- seq Analysis. Graham Etherington Sainsbury Laboratory Training Course http:// tsltraining.tsl.ac.uk /. Today's topics. The basics – What is RNA- seq , paired-end reads, alternative splicing Considerations before sequencing Library prep

570 views • 33 slides

RNA- Seq Lab

RNA- Seq Lab. Radhika S. Khetani. Powerpoint by Casey Hanson. Exercise. Use the Tuxedo Suite to: Align RNA- Seq reads using TopHat (splice-aware aligner). Perform reference-based transcriptome assembly with CuffLinks . Obtain a new transcriptome using CuffLinks & CuffMerge .

528 views • 30 slides

RNA seq (I)

RNA seq (I). Edouard Severing. A typical heat stress experiment ( climate change ). Economically important frog. Heat stress ( convection ). Control. 85 minutes. How does the frog adapt and survive?. 5 days. Coping with heat stress.

962 views • 64 slides

Biases in RNA- Seq data

Biases in RNA- Seq data . Transcript length bias. Two transcripts of length 50 and 100 have the same abundance in a control sample. The expression of both transcripts is doubled in a treatment sample. The biological variance is the same for both transcripts.

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Le RNA-seq

Le RNA-seq. L ’ article fondateur: Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 320:1344-1349. En un run, on générait en 2011 environ 15 million de séquences de 35 bp.

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Biases in RNA- Seq data October 30, 2013 NBIC Advanced RNA- Seq course

Biases in RNA- Seq data October 30, 2013 NBIC Advanced RNA- Seq course. Prof. dr. Antoine van Kampen Bioinformatics Laboratory Academic Medical Center Biosystems Data Analysis Group Swammerdam Institute for Life Sciences a.h.vankampen@amc.uva.nl.

1.43k views • 116 slides

RNA-seq experiences and plans LUMC

RNA-seq experiences and plans LUMC. Peter A.C. ’ t Hoen Human Genetics, LUMC. Pipelines. PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data Bioinformatics 28:479-86 (2012)

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“BIG DATA” from RNA- Seq Experiments

“BIG DATA” from RNA- Seq Experiments. Significance of RNA- Seq Approaches Reveals which genes are expressed and the levels at which they are expressed; a technique for the “post-genomic” era Of huge importance for biomedicine, toxicology, environmental biology, and basic research

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Bioinformatics for DNA - seq and RNA- seq experiments

Bioinformatics for DNA - seq and RNA- seq experiments. Li-San Wang Department of Pathology and Laboratory Medicine Penn Institute for Biomedical Informatics Penn Genome Frontiers Institute University of Pennsylvania Perelman School of Medicine. Next Generation Sequencing Technology.

483 views • 29 slides

RNA-Seq and transcriptome analysis

RNA-Seq and transcriptome analysis. Radhika S. Khetani, Ph.D. Technical Lead, User Support & Training High Performance Biological Computing (HPCBio) Roy J. Carver Biotechnology Center. RNA-Seq or Transcriptome Sequencing RNA-Seq It is the process of sequencing the transcriptome

1.24k views • 78 slides

RNA-seq data

Supplementary Fig 1. A. B. UCSC database (affyU133Plus2, knownGene ). Affymetrix microarray data (GENT database). RNA- seq data. RNA-seq data. Mapping with Tophat /Bowtie. Assembling by Cufflinks without -G option. Mapping with Tophat /Bowtie. Get lincRNA probe list

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RNA-Seq datasets

RNA-Seq datasets. Dan Lawson. New buzz word (old data). In the beginning there were ESTs... and then there was Roche 454.. and then Solexa/Illumina. Why do we generate data sets? Who is producing data sets? Where do we obtain these? What can we use them for? How do we organise these?.

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Bioinformatics Pipelines for RNA- Seq Data Analysis

Bioinformatics Pipelines for RNA- Seq Data Analysis. Ion M ă ndoiu and Sahar Al Seesi Computer Science & Engineering Department University of Connecticut. BIBM 2011 Tutorial. Outline. Background RNA- Seq read mapping Variant detection and genotyping from RNA- Seq reads

1.57k views • 112 slides

RNA-SEQ

ESTE ARTICULO ES MUY INTERESANTE HABLA DEL RNA SEQ

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How to Visualize Data With Google Data Studio

https://contentmarketinginstitute.com/2020/03/google-data-studio-visual-content/ Youu2019re familiar with Google Docs and Sheets, but have you used Google Data Studio? The free tool lets you turn data into eye-catching visuals and easy-to-read reports.

24 views • 1 slides

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