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URL: https://dx.doi.org/10.17504/protocols.io.qhedt3e

Authors: Frank Aylward

Summary: This is an example of a simple short read mapping analysis that could be used as part of a transcriptomics or RNA-seq workflow.  Code is intended for use on an Ubuntu 16.04 LTS OS, but it may work on other Unix or Unix-like systems.This tutorial uses data from the following very nice paper from the Hatfull group:Dedrick, Mavrich, Ng, and Hatfull, Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives. BMC Microbiology, 2017. https://doi.org/10.1186/s12866-017-1131-2The tools that are used include:SRA toolkit: https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtmlsamtools: http://samtools.sourceforge.net/BEDOPS: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/bam2bed.htmlBEDtools: https://bedtools.readthedocs.io/en/latest/Make sure that these tools are installed before starting the tutorial. On a Ubuntu OS you should be able to install most with "sudo apt install", but you may wish to use a package manager such as Anaconda or Miniconda as well. Throughout the tutorial some notes may be made about particular versions of tools. For example, note that the version of SRA toolkit that is installed with apt install often leads to downstream errors, it may be desirable to install this tool with Miniconda instead. Miniconda bash installers can be found here: https://conda.io/miniconda.html

Affiliations: Virginia Tech

Version: 3

Publication Date: 2018

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