EthanHolleman / BISanger

Estimate bisulfite conversion freqency from Sanger sequencing data

Estimate bisulfite conversion frequency based on Sanger sequencing data of converted PCR products.

Premise

Non-denaturing bisulfite treatment converts single stranded cytosine nucleotides to thyamine nucleotides. Treating a homogenous plasmid substate with bisulfite and PCR amplifying the resulting products will give you a new population of sequences with some degree of C -> T conversion.

Subjecting this population to Sanger sequencing allows us to estimate the efficiency of conversion by comparing relative C and T RFU values at potential conversion sites. The higher the ratio of T to C signal the greater the conversion at that site.

This requires processing, aligning and visualizing raw Sanger trace data. This Snakemake based workflow is designed to do just that.

Run the workflow

1. Install snakemake
2. Run snakemake -j 1 --configfile workflow/config.yml --use-conda from the root directory of the repo.