This is the git repository for the pipeline created by the UCSF PUBS2014 class to analyze data generated in the EMPIRC-BC experements of ubiquitin.
the piple line takes raw fastq files generated on Illumina deep sequencing platforms, counts Ub alleles, scores allele fitness, and generates a heatmap of allele fitness
the usage for each script in a module is found in the read me of each module and in the methods section of our publication.
cheers