PUBS
Python
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00_Subassembly
01_extract_counts
02_initial_score
03_toss_outliers
04_create_matrix
Caffeine_floored.csv
Caffeine_stdev.csv
DMSO_floored.csv
DMSO_mean_stdev.csv
DTT_floored.csv
DTT_stdev.csv
HU_floored.csv
HU_stdev.csv
MG132_floored.csv
MG132_stdev.csv
README.md

README.md

PUBS2014

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