Strand NGS-Calling narrow and broad peaks from ChIP-Seq data

Know about the state-of-the-art algorithms implemented in Strand NGS for detecting the binding sites of transcription factor (narrow peaks) and enriched regions of histone modification (broad peaks) from ChIP-Seq data. Read the benchmarking study on Calling narrow and broad peaks from ChIP-Seq data in Strand NGS by Rohit Gupta and Anita Sathyanarayanan. For more information, … Continue reading “Strand NGS-Calling narrow and broad peaks from ChIP-Seq data”

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Interesting findings by ChIP-Seq and DNA-Seq analysis using Strand NGS

The year 2014 was a great year with exciting features and enhancements updated in Strand NGS. We take this opportunity to thank our clientele and well-wishers for their support and feedback. We wish you all a happy and prosperous new year and look forward to a more fruitful engagement in 2015. In this blog on … Continue reading “Interesting findings by ChIP-Seq and DNA-Seq analysis using Strand NGS”

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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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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 I

Last month, as in my wont, I was taking a look at publications that had very recently used our software for analysis of NGS data. Of these, four were by groups who had used the RNA-Seq workflow from the Avadis NGS suite to run the analysis of their data. Intrigued by the fact that this … 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 I”

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A Sneak Peak at Avadis NGS Version 1.5’s New Features!

The release date for the next version of Avadis NGS is just around the corner. Not only does the software include a lot of refinements in some of the older features, but it also boasts of a number of cool new ones! So here is a sneak peak at some of these features in version … Continue reading “A Sneak Peak at Avadis NGS Version 1.5’s New Features!”

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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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