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Old 03-18-2014, 12:56 AM   #1
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Location: india

Join Date: Mar 2014
Posts: 8
Default samtools for beginners/biologists

Im a biologist, very newbie to bioinformatics tools.

I am interested in retrieving raw sequence data of all individuals
from different populations, with regards to a particular gene, for eg.
AGTR1 from the 1000genomes database. this requires me to use Data slicer in 1000genomes that will give the BAM files with alignment data in the region of the gene of interest.
To open BAM files I need to use samtools. However, I cannot find an exe file for samtools. then based on the treads of this forum, I read that one need to install cygwin, then install samtools from within cygwin. Or do I need a linux OS.

Could anyone please give some advice?

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Old 03-18-2014, 01:18 AM   #2
Location: Sri Lanka

Join Date: Mar 2014
Posts: 19

Majority of the open source bioinformatics tools are intended to be used on a unix based system. They do not contain executable files (.exe). To 'install' the softwares you need to 'build' them via bash scripting language using a terminal.

Cygwin provides a linux-type terminal for windows users to proceed with such situations but I would recommend you to start using a unix based system (typically linux or macOSX), as it would be much more hassle free when you are advancing in the field of bioinformatics with time.
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