Mapping RefSeq transcripts to the genome using UCSC

Transcript annotations are extensively used in NGS data analysis. In RNA-Seq, they are used at every step of the pipeline – to map spliced reads against the genome, perform quantification, detect novel exons etc. In DNA-Seq, they are used to predict the effect of variants detected in the sample. Clearly accurate transcript annotations are vital … Continue reading “Mapping RefSeq transcripts to the genome using UCSC”

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From yeast to mice to chicks to stem cells – 4 ways RNA-Seq analysis sheds light on the world around us (a four part series)- Part II

In my previous blog post, I had walked you through a yeast paper where the authors had mapped its mitochondrial trancriptome. They had used the RNA-Seq analysis tool from Avadis NGS in clever ways to figure out details about the transcriptome that played a key role in piecing together the final map. In this week’s … Continue reading “From yeast to mice to chicks to stem cells – 4 ways RNA-Seq analysis sheds light on the world around us (a four part series)- Part II”

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Benford’s Law and NGS Gene Counts

This may be a piece of trivia more than anything else, but anyway, let’s begin with the surprising part. Take any RNASeq sample and assign to each gene a count corresponding to the number of reads aligning to that gene (what we call Quantification in Avadis NGS). For the purposes of this post, ignore all … Continue reading “Benford’s Law and NGS Gene Counts”

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Welcome to our blog

Our goal for this blog is to be a distraction that is useful for you as well as for us. We will use this venue to express our bewilderment and discoveries as we traverse the genome. Mostly, we’ll geek out over puzzling challenges in bioinformatics, but we may also delve into other relevant topics – … Continue reading “Welcome to our blog”

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