◾ Building Program Pipelines
Learning goal: You can pass parameters to your programs and run other programs from Python. 14.1 IN THIS CHAPTER YOU WILL LEARN
• How to make programs work together
• How to run other programs from Python
• How to pass parameters to a Python program
• How to navigate directories from Python
14.2.1 Problem Description
For many research questions, one program is not enough. Oen, you need to make two or more programs work together. Next-generation sequencing (NGS) data analysis is a representative example. NGS technologies are today widely used to study dierential expression of genes, noncoding RNAs, mutations, and more. All NGS platforms perform massive parallel sequencing of cDNA or DNA molecules independently of the machine conguration and the chemistry used. In particular, they can be used to perform the “whole transcriptome shotgun sequencing” or RNA-seq, which consists of high-throughput cDNA sequencing aimed at collecting information about the RNA content of a sample.