Loops At Command Line

Loops can provide an efficient way to perform iterative actions at command line. This video provides a brief introduction to writing and executing "for loops" at command line, with a specific example of using Bowtie2 software to perform DNA sequence alignments for a series of files.

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To obtain the files and software needed to follow along, and to organize your working directory so that the code in the video should work as-is, do the following…

Download example input data files used in video at…

Download Bowtie2 software from the following link. Note you’ll need to run this on either a Mac or Linux platform. I used v 2.4.1 in the video.

Unzip the Bowtie2 file, move the resulting folder into your working directory, and rename it ‘Bowtie2’. Inside that folder there is an example/reference subfolder. Move the ‘reference’ folder and its contents (a single file named ‘lambda_virus.fa’) to your working directory, and rename the folder ‘ref’. Now index the reference with './bowtie2/bowtie2-build ref/lambda_virus.fa ref/lambda_virus'. At this point the working directory should contain the ‘Bowtie2’ folder, the ‘ref’ folder, and the 5 fastq input files.