Welcome to another bioinformatics blog
Welcome to another bioinformatics blog which is my first attempt to finally start sharing advice and pieces of code for everyday computational work, which is something that many others have done so...
View ArticleInstallation of UCSC Genome Browser in a local server
A. Preface and MySQL configurationThe UCSC Genome Browser is one of the most essential tools in genomics research. Its value is ever increasing, proportionally to the current explode in available Next...
View ArticleCreating track hubs for the UCSC genome browser with BAM files
One of the projects that I am currently involved deals with the detection of novel long non-coding RNAs regulating the WNT signaling pathway in colon cancer. Since we have had our own local...
View ArticleAdding permanent custom annotation tracks to a local UCSC Genome Browser...
As promised in the previous post, in this one, I will show how can one "hack" into the UCSC Genome Browser (local) MySQL database in order to create permanent tracks (annotation, signal or other). One...
View ArticleCreating stranded signal tracks for the UCSC Genome Browser
Recently, I was asked by one of my collegues if there was a way to display stranded wiggle signal files. A couple of years ago I would say that it is possible, however quite messy, as the only way to...
View ArticleIs Bioinformatics really hard?
I would like to share some thoughts that came to my mind today, after a specific event having to do with bioinformatics training. First of all, don't get confused by the title of the post. It might...
View ArticleConverting older SCARF format to FASTQ
Recently, I was asked by a collegue if I recognize the following raw data format coming from a quite old dataset which came out from the first next generation sequencers and relatively old software...
View Articlet-test with F-test for equality of variance
The t-test between two samples/biological conditions is still one of the most common statistical tests used for the detection of differentially expressed genes in microarray studies, even if a lot of...
View ArticleSummarizing microarray normalized probe expression to gene expression
The usual and fundumental result of the analysis of a microarray data experiment is a list of differentially expressed genes, always according to the statistical design and the biological questions...
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