diff --git a/README.md b/README.md index 8605d7f..6fd217b 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ cd OGT_prediction If you're on another OS, install all the python packages. Then install bedtools, tRNAscan-SE, barrnap, and prodigal; and all their dependencies. Create a file called external_tools.txt listing bedtools, tRNAscan-SE, barrnap, and prodigal tab separated from the absolute path for each executable. Copy this external_tools.txt file into the feature_calculation and prediction directories. ### OGT Data -To calculate regressions, a species_trait file (tab delimited) is required. The species_OGT file used for calculating regression in Sauer & Wang (2019) and found here, was originally published in Sauer et al. (2015). The species_OGT file is named "all_merged_12_10_2012.txt" and found within http://www.med.nyu.edu/skirball-lab/dwanglab/files/thermostability_v1.1.tar.gz. If new regression are calcuated using that species-OGT file, please cite: Sauer et al. Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical Journal (2015) https://doi.org/10.1016/j.bpj.2015.07.026. +To calculate regressions, a species_trait file (tab delimited) is required. The species_OGT file used for calculating regression in Sauer & Wang (2019) was originally published in Sauer et al. (2015). The species_OGT file is named "all_merged_12_10_2012.txt" and found within http://www.med.nyu.edu/skirball-lab/dwanglab/files/thermostability_v1.1.tar.gz. If new regressions are calcuated using that species-OGT file, please cite: Sauer et al. Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical Journal (2015) https://doi.org/10.1016/j.bpj.2015.07.026. ## Demonstration This uses the previously computed regression models to predict OGTs for a few species. Start within the prediction directory. diff --git a/regression/README.md b/regression/README.md index e8219aa..bdb3da5 100644 --- a/regression/README.md +++ b/regression/README.md @@ -16,4 +16,4 @@ python3 regression_pipeline.py species_trait_file training_testing_file species_ training_testing_file is a list of species annotated as either "train" or "test", tab separated. For the first run, using NONE will automatically assign 20% of the species to a test set and generate this file for future use. ## OGT Data -To calculate regressions, a species_trait file (tab delimited) is required. The species_OGT file used for calculating regression in Sauer & Wang (2019) and found here, was originally published in Sauer et al. (2015). The species_OGT file is named "all_merged_12_10_2012.txt" and found within http://www.med.nyu.edu/skirball-lab/dwanglab/files/thermostability_v1.1.tar.gz. If new regression are calcuated using that species-OGT file, please cite: Sauer et al. Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical Journal (2015) https://doi.org/10.1016/j.bpj.2015.07.026. +To calculate regressions, a species_trait file (tab delimited) is required. The species_OGT file used for calculating regression in Sauer & Wang (2019) was originally published in Sauer et al. (2015). The species_OGT file is named "all_merged_12_10_2012.txt" and found within http://www.med.nyu.edu/skirball-lab/dwanglab/files/thermostability_v1.1.tar.gz. If new regressions are calcuated using that species-OGT file, please cite: Sauer et al. Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical Journal (2015) https://doi.org/10.1016/j.bpj.2015.07.026.