Command Line Tools for Genomic Data Science

开始时间: 04/22/2022 持续时间: 4 weeks

所在平台: CourseraArchive

课程类别: 其他类别

大学或机构: Johns Hopkins University(约翰•霍普金斯大学)

课程主页: https://www.coursera.org/course/gencommand

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课程详情

This class will cover an introduction to command line tools for managing genomic data. It will start with basic Unix commands for managing files and directories, followed by a review of the main starndardized data formats and hands-on instruction on how to use popular tools such as Samtools, Bedtools, Bowtie, and application specific technologies such as Bcftools and Cufflinks.

课程大纲

  1. Unix commands
    • Basic commands
    • Pipes
  2. Sequences and genomic features
    • Formats: Fastq, BED, GTF, SAM
    • Tools: Samtools, Bedtools
  3. Alignment and sequence variation
    • Bowtie, BWA
    • Samtools, Bcftools
    • Application: variant calling
  4. Transcriptomics
    • Tophat
    • Cufflinks
    • IGV
    • Application: RNA-seq analysis

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课程简介

Introduces to the commands that you need to manage and analyze directories, files, and large sets of genomic data. This is the fourth course in the Genomic Big Data Science Specialization from Johns Hopkins University.

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