Step 0: Get Started

MATALB environment

• Please follow the installation guidelines to download HiTRACE scripts, and register to MATLAB path.

• For all of the commands used, use help func_name to retrieve help information on syntax usage.

Best Practice

For a standard HiTRACE analysis, we recommend the following files as conclusive end-points:

• A saved workspace .mat file for analysis reuse.

• A saved script .m file for command records.

• A saved text-based .rdat file for sharing.

• Annotated figures for raw (gel) data and sequence assignment (see print_xsel_split in Step #8).

In other words, you should have the .mat workspace, .m script and .eps figures on your disk once you finished analysis, just like the ones from the provided example and shown in this tutorial series.

Thus please save your work frequently! Also organize your scripts. We recommend running save command often to save your workspace into .mat files in case of unexpected MATLAB termination. Please familiarize with commands like load, clear, close, which too.

Data Display

• Note that throughout the analysis, the electrophoretic traces are aligned vertically, so that higher mobility products (which pass the sequencer detector first) show up at the top.

This is basically historical; note that most biochemical papers take a different convention where the faster products are at the bottom, and in some of our papers, we show the traces aligned horizontally (this wasted the least space for early data sets like this mutate/map study).

Citations

• Papers describing the HiTRACE method (Yoon et al. 2011), background subtraction, ‘overmodification’ correction, and error analyses (Kladwang et al. 2014), online version of HiTRACE (Kim et al. 2013), and new auto-assign algorithm (Lee et al. 2015) are listed as reference. Please cite accordingly.

• Please report problems to rhiju@stanford.edu. So we can fix them!