Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. Pathogen Portal's RNA-Sequence Analysis Pipeline Part 1. Metaseq: a Python framework for integrating sequencing analyses; SciPy 2013 Presentation. RNA-Seq. ?utm_source=dlvr. Rrnaseq.pdf?utm_source=dlvr. NGSwatch: Next Generation Sequencing Watch — Watching Next-Gen Sequencing Grow One Publication At A Time. RNA-Seq 101.
RNA-Seq, one of the applications of Next-gen sequencing technologies, has completely changed the landscape of how we study gene expression. Here is our effort to compile all basic and review papers focus on RNA-Seq technology and applications of RNA-Seq technology. Early Papers on RNA-Seq The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing, Ugrappa Nagalakshmi, Zhong Wang, Karl Waern, Chong Shou, Debasish Raha, Mark Gerstein, and Michael Snyder, Science. June 6; 320(5881): 1344–1349, 2008. RNA-Seq Review Papers RNA-Seq: a revolutionary tool for transcriptomics.
RNA-Seq Method Papers TopHat: discovering splice junctions with RNA-Seq, Cole Trapnell, Lior Pachter and Steven L. Expression QTL Papers Using RNA-Seq Data Understanding mechanisms underlying human gene expression variation with RNA sequencing, Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. .Nature. RNA Editing Papers using RNA-Seq Data. Welcome to RNA-Seq Course’s documentation! — RNA-Seq Course v1.0 documentation. Fusioncatcher - Fusion Genes Finder for RNA-seq data. FusionCatcher and its installation script (which is bootstrap.py) may be downloaded from here!
FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq) from diseased samples. The aims of FusionCatcher are: FusionCatcher has been used originally for finding novel and known fusion genes in breast tumor cell lines BT474, SKBR3, MCF7, KPL4 as shown in the following articles: S. Kangaspeska, S. Hultsch, H. Edgren, D. Output example with the fusion genes found by FusionCatcher in the breast tumor cell lines (from the above articles) are: here for BT474 cell line here for KPL4 cell line here for MCF7 cell line here for SKBR3 cell line FusionCatcher has been cited in the following articles: JN. FusionCatcher has found novel FGFR2 fusion genes in SNU-16 and KATOIII gastric cancer cell lines! Complete version history can be found here. D. Differential Isoform Expression With RNA-Seq: Are We Really There Yet?
In case you missed it, a new paper was published in Nature Biotechnology on a method for detecting isoform-level differential expression with RNA-seq Data: Trapnell, Cole, et al. "Differential analysis of gene regulation at transcript resolution with RNA-seq. " Nature Biotechnology (2012). RNA-seq enables transcript-level resolution of gene expression, but there is no proven methodology for simultaneously accounting for biological variability across replicates and uncertainty in mapping fragments to isoforms. One of the most commonly used workflows is to map reads with a tool like Tophat or STAR, use a tool like HTSeq to count the number of reads overlapping a gene, then use a negative-binomial count-based approach such as edgeR or DESeq to assess differential expression at the gene level.
Figure 1 in the paper illustrates the problem with existing approaches, which only count the number of fragments originating from either the entire gene or constitutive exons only. NGS Leaders Event :: Webinar: Methods for RNA-Seq Data Analysis. Upcoming Events Event Details: November 15, 2012 Webinar: Methods for RNA-Seq Data Analysis Originally aired November 15, 2012 RNA-seq is one of the most recent and sophisticated tools to study transcriptome changes through massively parallel sequencing, however understanding and managing the data generated from RNA-Seq presents unique challenges. I-Study: Genomic Interpretation - Who Will Pay? During this webinar, members of the study review team present preliminary findings of the I-Study, conducted at the Harvard Medical School's 2011 Personalized Medicine Conference.
Archived Events Feb Bio-Inspired Materials - Using Genomics to Engineer Recyclable Materials An exclusive FREE webinar hosted by Cambridge Healthtech Associates™. Date: February 25, 2014 Time: 11:00AM (EST) Dec Clinical Genomics & Informatics Europe Lisbon, Portugal, Dec 4-6. Nov Metagenomics, Microbiomes, and Models...Oh My! A webinar by experts in the field of metagenomics. Back to Basics - An Overview of RNA-Seq Sep Aug Jul May View All. NGSLeaders:: A Community for Next Generation Sequencing Pioneers.