This pipeline processes barcode counts sequenced from twelve fluorescence-activated cell sorting (FACS) samples of the synTCS-MutLib strain in the fumarate condition. Sequence data was generated using the Illumina NextSeq platform using paired-end sequencing read amplicons. Raw sequencing data was pre-processed on a high-performance computer using the Makefile script available in the project GitHub repository. Here, pre-processed barcode-count files for all twelve fumarate samples are merged, adjusted abundances are computed using the protocol from Biswas et al., (2021), and a median activation score- here, "median bin"- is calculated for each observed barcode. This analysis is replicated for the No Ligand and Aspartate samples.

This pipeline processes barcode-sequence-phenotype data previously generated in Merge_and_MEFL_Convert.Rmd and determines which multi-barcoded mutnts have significant differences between their fold-change scores.

This pipeline processes and visualizes barcode-sequence-phenotype data previously generated in Merge_and_MEFL_Convert.Rmd.

This pipeline processes barcode counts sequenced from twelve fluroescence-activated cell sorting (FACS) samples of the synTCS-MutLib strain in the aspartate condition. Sequence data was generated using the Illumina NextSeq platform using paired-end sequencing read amplicons. Raw sequencing data was pre-processed on a high-performance computer using the Makefile script available in the project GitHub repository. Here, pre-processed barcode-count files for all twelve aspartate samples are merged, adjusted abundances are computed using the protocol from Biswas et al., (2021), and a median activation score- here, "median bin"- is calculated for each observed barcode. This analysis is replicated for the No Ligand and Fumarate samples.

This pipeline processes barcode counts sequenced from twelve fluroescence-activated cell sorting (FACS) samples of the synTCS-MutLib strain in the no ligand condition. Sequence data was generated using the Illumina NextSeq platform using paired-end sequencing read amplicons. Raw sequencing data was pre-processed on a high-performance computer using the Makefile script available in the project GitHub repository. Here, pre-processed barcode-count files for all twelve no ligand samples are merged, adjusted abundances are computed using the protocol from Biswas et al., (2021), and a median activation score- here, "median bin"- is calculated for each observed barcode. This analysis is replicated for the Fumarate and Aspartate samples.

This pipeline processes barcode-sequence-phenotype data previously generated in Merge_and_MEFL_Convert.Rmd and determines positions which are significantly enriched for influencing aspartate responsiveness and specificity based on the total number of barcodes observed.

This pipeline processes all barcode-sequence pairs and their associated median bin scores for all three conditions. Here, previously generated files for all three conditions (containing barcodes, their associated nucleotide and amino acid sequences, activation ("median bin") scores, the lower and upper indices of their activation bins) are merged. Median bin scores are then converted to molecules of equivalent fluorescein (MEFL).