Wiggles files are a way to visualize read data mapped to the genome. This document is a walk through onto how to make wiggle files. To visualize wiggles you need to use Gbrowse which can either be installed on a local web server, or can use publicly available UCSC Genome Browser. With the UCSC Genome Browser for viewing large wiggle files, it works better if you put the wiggle files on a publicly available web server and provide the URL instead of trying to upload the file.
Create pileups from bowtie SAM files
View tracks on UCSC Genome Browser: http://genome.ucsc.edu/
If mean values are desired continue with the following parts:
Place wiggle files into the "data" folder with the naming format:
<Name>-ln1.wig <Name>-ln2.wig <Name>-ln3.wig etc.
Run combine_wigs.sh. This will combine all of the wiggles files into one file and flag them by and lane
Edit wiggle.sas specifically lines 5, 32, 38, 42, 46 to fit specific needs
Take sas output and run it though make_means_wiggle.sh Note: first edit this file for specific needs
Finally visualize using UCSC Genome Browser
Wiggle tracks produced by viewers such as UCSC are not always the highest resolution images. The R-project is a capable alternative for making wiggle tracks.
A series of functions have been created wiggleplot_function.R. These functions can be used to create a both wiggle plots and add features such as gene models to the graphs. Here is a script that has some example usage wiggleplots_example.R.