Technology

The Pitfalls of RNA-Seq Methodology

The Pitfalls of RNA-Seq Methodology

TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to ...

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Rascaf – Improving Genome Assembly with RNA Sequencing Data

Rascaf – Improving Genome Assembly with RNA Sequencing Data

Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. ...

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Strategies to Identify Natural Antisense Transcripts

Strategies to Identify Natural Antisense Transcripts

Natural antisense transcripts, originally considered as transcriptional noises arising from so-called “junk DNA”, are recently recognized as important modulators for gene regulation. They are prevalent in nearly all realms of life and have been found to modulate gene expression positively ...

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Docker Pipelines for RNA-Seq Alignment and Analyses

Docker Pipelines for RNA-Seq Alignment and Analyses

Background: Docker (https://www.docker.com) is an application that packages binary executables and scripts into modules (containers) with their software dependencies. Containers can be freely mixed and matched to form workflows that give identical results on any platform which supports Docker. The ...

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