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- Davo on DESeq vs. edgeR vs. baySeq
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- Davo on Perl and SAM
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Author Archives: Davo
Using blat
My multipurpose sequence aligner tool of choice for many years has been blat. This is just a short post on the very basics of blat. Below is a slide I made couple of years ago: First blat splits the reference … Continue reading
Getting started with TopHat
I will use RNA-Seq data from Marioni et al., 2008 Genome Research to test TopHat. I found it funny that the submission title for their dataset was “RNASeq: the death Knell of expression arrays?”; I guess they decided to go … Continue reading
Getting started with Circos
Getting Circos working on Ubuntu. For more information, see http://circos.ca/software/download/circos/.
Equivalents in R, Python and Perl
I’ve used Perl the most and find myself using R more and more due to the statistical packages. It seems that more and more people are switching from Perl to Python, as least in bioinformatics, thus I’ve started this page … Continue reading
Creating UCSC Genome Browser custom tracks with links
An extremely useful feature of the UCSC Genome Browser, which I have been using for many years, is the ability to create links your genomic features in your custom track. For more information, see this page, step 5. For example, … Continue reading
Learning to use biomaRt
In the past I’ve been manually downloading tables of data annoation and parsing them with Perl. I guess it’s time to do things more elegantly. Below is code taken from the biomaRt vignette: The vignette contains other cool examples, which … Continue reading
Making a barplot in R
Just a short post on making barplots in R after reading in data via the read.table() function. I created a file with two rows, the first row containing the header and the second row containing the data values. a b … Continue reading
Comparing different distributions
I recently learned of the Kolmogorov-Smirnov Test and how one can use it to test whether two datasets are likely to be different. Strictly speaking, the p-value gives us a probability of whether or not we can reject the null … Continue reading
Today while reading a paper, I found some interesting one-liner facts. They are way too short to create a post on but I would like to make a repository of them. What better place to store these facts than Twitter! … Continue reading
Variance in RNA-Seq data
Using data from this paper. Generate some random data from Poisson distribution