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Querying the Cancer Transcriptome

from Genetic Engineering News by Richard A. Stein, M.D., Ph.D. The complex and dynamic transcriptional patterns unveiled by the ENCyclopedia of DNA Elements (ENCODE) project, together with the finding that less than 2% of the transcriptional output of the human ...

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STAR: ultrafast universal RNA-seq aligner

To align their large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, a team of researchers at Cold Spring Harbor Laboratory developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses ...

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RNA-Seq making significant contributions to GENCODE project

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been ...

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How Many Reads are Enough?

There is no question that RNA-Seq has several major advantages over current hybridization-based approach such as microarrays. However, with the cost per sample of RNA-Seq still much higher than microarray, it would be beneficial if multiple samples could be multiplexed ...

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Another weapon in the war against bias

There have been several studies demonstrating the biases inherent to the RNA-Seq method as well as variation in results across protocols and platforms. Researchers have set about innovating methods to correct for these biases and variances, but until now, most ...

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Best Practices for RNA-Seq

The ENCODE Consortium has finalized Standards, Guidelines and Best Practices for RNA-Seq V1.0 Download the document RNA-Seq is a directed experimental approach aimed at characterizing transcription in biological samples. This document presents a set of guidelines and standards focused on ...

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