My notes on the sequence/quality data from Illumina genome analyser.
Phred
Phred is a program that takes the trace files produced by traditional DNA sequencing, calls the bases and assigns a quality value to each called base.
It calculates a score for each base as:
Qphred = -10 x log10(1/$error_prob)
Where $error_prob is the probability of the base call [...]
My notes on how Macs works. Probably riddled with errors – check out the links below for official docs:
Website
Genome Biology Paper
We’ve used ChIP to grab bits of DNA that correspond to the region bound by the transcription factor (or marked by the histone modification, or whatever). So the data looks something like this:
Except that the [...]
At ISMB, the Galaxy guys were talking about using Galaxy as an interface for analysing NGS data. I’m having a go at getting it up and running on EC2. Notes are really for my own reference, but I thought I’d post them in case they were of use to anyone else.
AWS Setup
Obviously, you need an [...]