Monthly Archives: April 2012

RNA-Seq Enabling Proteomic Studies

Effective proteome profiling is generally considered to depend heavily on the availability of a high-quality DNA reference database. As such, proteomics has long been taxonomically restricted, with limited inroads being made into the proteomes of “non-model” organisms. However, next generation ...

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RNA-SeQC for RNA-Seq Datasets

RNA-SeQC is a program which provides key measures of data quality for RNA-seq datasets. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron, intragenic), continuity of coverage, 3’/5’ bias, and count of ...

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Upcoming RNA-Seq Workshop

Berkeley *Seq I: Tools and Workflows for RNA-Seq Analysis Saturday, June 30, 2012 9 a.m. – 5 p.m. 105 Stanley Hall University of California, Berkeley REGISTER BY JUNE 7 Berkeley *Seq I, the inaugural workshop on analysis of Next ...

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RSeQC – RNA-seq quality control package

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation ...

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RNA-Seq Abstracts – Experimental Biology 2012

SUNDAY NUTRITION 4:00 128.5 RNA-Seq analysis of placental gene expression: effect of maternal obesity. K. Shankar, Y. Zhong, P. Kang, M.J. Ronis and H. Gomez-Acevedo. Arkansas Children’s Nutr. Ctr., Little Rock. SUNDAY NUTRITION C307 II 647.10 An RNA-Seq approach to ...

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MapAl – a tool for RNA-Seq expression profiling

MapAl is a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number of reliably measured ...

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