Ask about isoforms.fpkm_tracking file

[nhuhoa]

Dear Jeff Moffitt, and developers,
Thanks for the very useful package.

I am Hoa Tran, a postdoc from Aparicio Lab. I am currently working on the pipeline for the design and construction of MERFISH probes, and I have a small question regarding isoform file (I am a beginner in DNA sequencing analysis)

In your script of library design, you need an isoform file as input.
https://github.com/ZhuangLab/MERFISH_analysis/blob/master/example_scripts/library_design_example.m
And in README.txt of MERFISH_Example2/ folder that you used to run scripts:
isoforms.fpkm_tracking -- The output of cufflinks when run on published RNA-seq data from the U-2 OS cell line: GEO accession GSM1231610/SRR987281.

My question is do I need to build a new isoform file or can I use the existing one here that you provided in Example2/ folder? I tend to construct a new gene panel for breast cancer human cells and test the designed panel with merfish experiment.

Thanks,
Hoa Tran