Venn Diagrams Simplified

Not a week goes by without me having to compare multiple lists to evaluate overlap. Re-analyzing any data and comparing that with previously computed data, comparing results from multiple tools or multiple samples. Sometimes the unix commands diff, paste and join come handy, but most times am looking for some additional information. Almost always, am [...]


R Line Plots – the easiest fastest plot ever

What you need: Data R Eager Bioinformatician For data I used a file with 7 columns where the first column was a counter and the other columns (2-7) had different values that I would like to compare across using a line plot to visualize the variation in my data points Serves: As many data points [...]

How recent are rare variants?

The Department of Genome Sciences at the University of Washington in Seattle, in a multi-institutional effort sequenced 15,336 genes for the NHLBI sponsored ESP project from a total of 6515 individuals of European American and African American descent.To identify approaches for disease-gene discovery, its important to understand evolutionary history of homosapiens and identify the age [...]

Journal Club: False-positive signals in exome sequencing

Detecting false-positive signals in exome sequencing Human Mutation I cannot believe that this paper is already a year old. There was a printed copy on my desk, but never got transmitted from the eyes into the brain!! Finally, there was enough time to review the paper and collate all the valuable information to share here. [...]

Journal Club: Indels in 179 genomes (1000genome data)

The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes Genome Research Finally there is a comprehensive analysis on indels, and of course it is the Next Generation Sequencing data that is driving it. I have my concerns with the biases of NGS technology and analysis along with ensuing false-positives [...]

AGBT 2013 Saturday sessions

Plenary Session: Genomic Technologies Len Pennacchio, Lawrence Berkeley National Laboratory, Chair -- could not take notes on some of the talks and afternoon session 9:00 a.m. – 9:30 a.m. Rebecca Leary, Johns Hopkins Kimmel Cancer Center “Personalized Approaches to Non-invasive Cancer Detection” - personalized analysis of rearranged ends (PARE)-identify structural alterations in solid tumors - [...]

AGBT 2013 Friday sessions

Plenary Session:  Genomic Studies II John McPherson, Ontario Institute for Cancer Research, Chair 9:00 a.m. – 9:30 a.m. Steve Scherer, The Hospital for Sick Children “Whole Genome Sequencing Analysis in Autism” - Autism Spectrum Disorder (ASD) - high heritability, familial clustering & ~4:1 male to female bias (as many candidates on X-chr) - 100+ risk [...]