discovering nice software

I recently had the need to do some flow cytometry. This being a new skill to me I had trials and errors in getting my lab protocols to work.

Once I had my technique working okay I was able to save my data as .fcs files. I saved my files and then began searching for proprietary-free software to use to process the data.

I have found some excellent software called Flowing Software 2.5.1 by Perttu Terho of the University of Turku, Finland.

http://flowingsoftware.btk.fi/

This software includes a nice clean visual work flow, reminiscent of Orange, with its connecting arrows.

https://orange.biolab.si/

Very helpful, though perhaps could have included some calculation tools or the ability to smooth out histograms (and change the colours).

Always grateful to these software developers though!

awk saves the day…

Sometimes you just need to process your text data in some manner.

I was looking for a simple script to count raw reads within my fastq files and came across this helpful script in Biostars by Jorge Amigo (thank you Jorge).

awk ‘{s++}END{print s/4}’ file.fastq

This counts the number of lines and divides by 4 to output the number of raw reads.