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Teach/Resource/GalaxyNGS101

Galaxy NGS 101 Videos

Resource

Galaxy NGS 101

Types
Tutorial
Domains

RNA-Seq, Variation, Quality Control

Owners

Galaxy Project

Formats
Web Pages, Screencasts
Date
2015/06

This set of exercises is designed to serve as a comprehensive resource describing manipulation and analysis of NGS data. While it is designed to highlight the utility of Galaxy it will also provide information that is broadly applicable and can be used for teaching of big data biology. It is accompanied by a collection of screencasts.

The new Galaxy NGS 101 Tutorial was published this spring and introduces a wide range of topics related to analyzing next generation sequencing data with Galaxy. We are happy to announce that videos to accompany this tutorial are now online as well. The 20 videos cover:

  1. Uploading data from your computer

  2. Uploading data from FTP

  3. Uploading data from the Web

  4. Uploading data from EBI SRA

  5. Uploading data from NCBI SRA

  6. QC'ing with FastQC

  7. A quick into to read mapping

  8. Mapping to YOUR reference

  9. Tweaking BAM

  10. Non-diploid variant calling with NVC

  11. Non-diploid varinat calling with FreeBayes

  12. Looking at multiple datasets in IGV

  13. Calling variants with FreeBayes

  14. RNA-Seq: Mapping with TopHat

  15. RNA-Seq: Assembling and quantifying transcripts with CuffLinks

  16. RNA-Seq: Playing with CuffDiff output and Cummerbund to find differentially expressed transcripts

There are also 4 new videos that provide an overview of different sequencing platforms:

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