Story: IGBF-251 (make link.psl files for human arrays)
Date: November 4, 2014

Intro: A user has requested the ability to visualize probe sets within IGB but first some code had to be written to make link.psl files from blat output. The code has been written and this story is now ready for testing.

Story IGBF-251 was tested on:
*IGB Version: 8.1.11
-(My Office Windows) Windows 7 Enterprise 2009 Service Pack 1 using JRE version 1.7.0_67-b01 Java HotSpot(TM) Client VM

The story was tested using this workflow:
1) I downloaded the "lorainelab-affyprobesetsforigb-ba69f060ef56" from git repo.
2) I opened the link.psl.gz file in IGB.
3) I checked that probe sequences matched. I used the probe tab file to look up probe sequences and compared pink boxes to zoomed-in genome sequence.
4) I googled probe sets to verify that genes probe sets matched the genes.

Observed:
All points passed. = PASS

Summary:
Story IGBF-251 was tested on my office Windows. My observations were in accordance with the IGB Team's expectations.

Assigning to Mason for testing.

To test, download zip file from git repo:

https://bitbucket.org/lorainelab/affyprobesetsforigb

Or...just clone it onto your desktop using git. (Ask Tarun how.)

Open the link.psl.gz file in "results" folder.

Check that probe sequences match. Use the probe tab file to look up probe sequences and compare pink boxes to zoomed-in genome sequence. They should match. Watch for off-by-one errors.

Also, google-search probe sets. In general, they should be located on top of genes the internet thinks these probe sets interrogate. Watch out for errors.