Serine-recombinase Assisted Genome Engineering - Relative Transcriptional Profiling (SAGE-RTP) Toolkit
The SAGE-RTP toolkit leverages source code from previously reported DNA regulatory element analysis package DRAFTS, providing new modification features adapted to accept nucleotide sequences and Illumina read length differences, for data process workflows utilizing DNA and RNA barcode counts for statistical analysis of sequence promoter expression levels with data visualizations.
- Run Pre-processing.ipynb notebook to create folder structure compatible with DRAFTS scripts
- Requires 'home_dir' path to Illumina DNA/RNA barcode reads
- Requires path to 01_DRAFTS_process_raw.sh
- Required bbmap installation (prerequisite for DRAFTS)
- Outputs Paired sequence data
- Run run_DRAFTS_DNA_v2.py to count DNA barcodes
- Run run_DRAFTS_RNA_v2.py to count RNA barcodes
- Run Build_tx_read_dataframe.ipynb notebook to calculate promoter-specific relative transcriptional activity (rta)
- Robert G. Egbert, & Joshua R. Elmore. (2022). Serine Recombinase-Assisted Genome Engineering - Relative Transcriptional Profiling (SAGE-RTP) Toolkit (1.0). Zenodo. https://doi.org/10.5281/zenodo.7388406
- Elmore JR, Dexter GN, Baldino H, Huenemann JD, Francis R, Peabody GL 5th, Martinez-Baird J, Riley LA, Simmons T, Coleman-Derr D, Guss AM, Egbert RG. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Sci Adv. 2023 Mar 10;9(10):eade1285. doi: 10.1126/sciadv.ade1285. Epub 2023 Mar 10. PMID:36897939; PMCID:PMC10005180.