Use a regular expression for filtering sequences by id from a FASTA file, e.g. just certain chromosomes from a genome. There are other tools as part of bigger packages to install (and no regex support), mostly awk-based awkward (sorry for the pun) bash solutions, and scripts using packages that one needs to install and with still no support for regular expressions. This however is a simple, straightforward little python script for a simple task. It doesn’t do anything else and doesn’t need anything but a stock python installation. Based on the FASTA reader snippet.  Continue reading →

An R script for those who like to be close to their qPCR data and catch problems early. It takes export files (multicomponent data, text format, “across columns”) of Life Technologies StepOne machines.

A standard analysis can be done in less than 5 minutes. It consists of these steps:
– plotting of the raw signal (and saving of the result) to catch odd amplification and strong offsets
– baseline correction
– magnified plotting (and save) to check correction and drift in signal
– cycle estimation by using a threshold
– tabulation of the results

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