HCR probe generator

This code is an add-on to https://github.com/rwnull/insitu_probe_generator

Create python environment and activate:

conda create -n hcr_probe_generator -c bioconda biopython numpy=1.23.5 pandas=1.3.5 blast openpyxl

Use batch_probe_generator.ipynb to generate HCR probes for all genes, listed in a csv file.

1. Create a google or excel sheet of your targets:

   • required headers: 'short','gene_name','amplifier','reference','sequence'
   • short: abbreveation for species name: e.g. dr for Danio rerio
   • optionally add more columns, if suited for your documentation

2. Export sheet as .csv file and place into the targets folder

3. Open the jupyter notebook "batch_probe_generator.ipynb", set the project name and adjust the folder paths to this repository

   • project name: same as the name of the targets.csv file, but without the ".csv".
   • paths are specific to your computer, depends where you placed this repository

4. Download and paste the required BLAST reference files in the references folder:

   • extract the file; should end with .fa

5. Run all the cells in the notebook "batch_probe_generator.ipynb"

   • make sure you have created and selected the correct python environment
   • see beginning of notebook for creating the conda environment

6. Find your HCR probes in the generated_probes folder

   • contains also the .xlsx file to upload to IDT with all the generated oligo pools