TAURUS-MH (Two-step Alignment with Unmapped Reads Using read Splitting for Methyl-HiC) is a mapping pipeline for methyl-3C/methyl-HiC data using a hybrid of ungapped and manual read splitting alignments with Bismark and Bowtie1. TAURUS-MH is dependent on Bismark, Bowtie1, PICARD, python, and pysam (a python module).
To install TAURUS-MH, Simply download all the python codes and run: python Install.py The Install program will ask you path to picard, bismark, bowtie, and python. Please provide correct path to these.
After the installation, TAURUS-MH.py will be generated.
Before the alignment, you have to prepare reference genome by: /bismark_folder/bismark_genome_preparation --bowtie1 --path_to_bowtie <Path_to_bowtie1> --verbose <genome_folder>
After the Installation and genome preparation, you can run TAURUS-MH with cmd: python TAURUS-MH.py <genome_folder> G_to_A_converted_mate C_to_T_converted mate