analyze bacterial surface display NGS data sets
step 1)
Use NGMerge (https://github.com/jsh58/NGmerge) to align and merge forward and reverse .fastq files
One at a time:
/NGmerge -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz -o sample_merged.fastq.gz
Or use recursive_loop.gz.sh to automate it
step 2)
identify correctly expressed and read bacterial clones
One at a time:
NGS_pattern_finder_combined.py
Or use recursive_loop_aligned.sh to automate it
step 3)
combine individual read files into a single dataframe object for analysis
Use NGS_merge.py and merge.sh
step 4) filter merged reads by quality (gate score, read counts, etc.) using reads_plots.py
step 4a)
read counts per round of sorting: analyze data using analysis_script.py
step 4b)
analyze SORTCERY data using reads_plots.py analyze gate scores using gate_score_analysis.py
step 5)
machine learning - explore models and performance using ml_script.py
step 6)
perform ILP - ILP_order2.py