sc2-sequencing/illumina

Illumina

FASTQ Downloader

This script downloads all FASTQs associated with a specific Run ID from Illumina's Basespace.

Usage

To be run in Cygwin

dl-fastqs.sh

The script will prompt for a Run ID. Copy the Run ID from the URL in Illumina Basespace.

Note that Ctrl+V does not paste in either Cygwin or Windows terminals. Use right-click, instead.

Installation

This script requires Cygwin. The install process is complicated thanks to requiring native features of both Windows and Cygwin.

1. Download and install Cygwin

   1. Select "Just Me" when asked who to install for
   2. Find and add the latest version of the "git" packages
   3. All other default options will work

2. Press Win+X, then I to open a new PowerShell window

3. Run wget 'https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-windows/bs.exe?bt_package=latest' -O $env:LOCALAPPDATA\Microsoft\WindowsApps\bs.exe

4. Close PowerShell

5. Open Cygwin Console and run

   BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
   $BS auth
   

6. Copy the given link, navigate to it in a browser, and login to Illumina Basespace

7. In Cygwin console now run

   git clone https://github.com/MillironX/sc2-sequencing.git
   cp sc2-sequencing/illumina/dl-fastqs.sh ~
   chmod +x dl-fastqs.sh
   

8. Right-click the Windows desktop, and click "New | Shortcut..."

9. Type C:\cygwin64\bin\bash.exe and click Next

10. Type Download Illumina Run or something else memorable and click "Finish"

11. Right-click the newly created shortcut and click Properties

12. In the Target textbox, add a space and --login dl-fastqs.sh to the existing text

13. Click OK

FASTQ Sorters

These scripts change the file names of the FASTQ files to correspond with the well positions during prep phases.

Usage

To be run with Julia.

julia --project=PATH_TO_ILLUMINA_FOLDER PATH_TO_SORTING_SCRIPT

In practice, this looks like

julia --project=C:\Users\MillironX\illumina C:\Users\MillironX\illumina\sort-miseq.jl

Installation

These scripts require Julia.

1. Download and install Julia
   1. Select "Add Julia to PATH" as an option
   2. All other default options will work
2. Download the Repo's ZIP file (click green button on upper-right)
3. Press Win+R, type %USERPROFILE% and press Enter
4. Copy the illumina folder from the ZIP file into the newly opened folder
5. Press Win+X, then I to open a new PowerShell window
6. Type julia --project=$env:USERPROFILE\illumina and press Enter
7. Press the ] key, the prompt should change to say (illumina) pkg>
8. Run instantiate
9. Press the backspace key to return to the julia> prompt
10. Run exit()
11. Close PowerShell
12. Right-click the Windows desktop, and click "New | Shortcut..."
13. Type julia --project=%USERPROFILE%\illumina %USERPROFILE%\illumina\sort-miseq.jl and click Next
14. Type Sort MiSeq Run or something else memorable and click "Finish"
15. Right-click the Windows desktop, and click "New | Shortcut..."
16. Type julia --project=%USERPROFILE%\illumina %USERPROFILE%\illumina\sort-nextseq.jl and click Next
17. Type Sort NextSeq Run or something else memorable and click "Finish"