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IGV Desktop User Guide Reorg

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helgathorv edited this page Oct 7, 2022 · 3 revisions

THE IGV DESKTOP USER GUIDE

(Separate files or one big file?)

  1. The IGV Basics (Note this section should not go into too much detail - meant to be an overview)

    1. What is IGV?

    2. Installing and launching IGV

    3. The IGV window

    4. The reference genome and data tracks

    5. About loading data (local files, URLs, google cloud, aws, indexed files, where does the data come from / go)

    6. Setting preferences and track options

    7. Navigating the view

    8. Sessions <maybe not in basics>

    9. The “igv” folder

    10. Getting help

      1. How to use igv-help forum and igv-team email

      2. Note that we don’t help wrt the science or interpreting the data. Point out some other forums for those types of questions.

      3. When to get local IT help

  2. The Reference Genome

    1. Loading the reference genome

      1. Hosted genomes

      2. Other genomes

    2. Managing the genome menu

    3. Something about the igv/genomes folder

    4. Viewing the reference genome

      1. Sequence track

      2. Gene annotation track

  3. Data Types

    1. Numeric data

    2. Genomic features

    3. Aligned sequencing data

      1. Basics

      2. RNA-seq

      3. 3rd gen / long reads

    4. Called variants

      1. MUT/MAF

      2. VCF

    5. Segmented copy number

    6. GWAS data

    7. RNA secondary structure

    8. Other

  4. Loading and Using Sample Attributes

    1. Loading sample attributes

    2. Sorting, grouping, filtering tracks by attribute

  5. Navigating the View

    1. Zoom in/out

    2. Scroll / pan

    3. Jump to locus

    4. Using a file to define

    5. Viewing multiple regions

    6. Regions of interest

      1. Defining regions of interest

      2. Viewing regions of interest

  6. Preferences

    1. View > Preferences

    2. Prefs.properties file

  7. Sessions

    1. New

    2. Save

    3. Load

    4. Reload

    5. Session format

  8. Saving images of the IGV view

    1. From the File menu

    2. From a batch script

  9. The Tools Menu

    1. Run batch script

    2. Run igvtools

    3. Find motif

    4. Run BLAT

    5. Combine data tracks

  10. External Control of IGV

    1. Controlling IGV from a different application through a port

    2. Running IGV with a batch file

    3. Controlling IGV through URLs

  11. Configuring user-hosted genomes and data

  12. igvtools

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