MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations

The file "data.tar" contains the output of the MADDD-seq pipepline. There is one sub-folder per sample. For each sample, the most important files are:

max_variants_2.adduct.gtf : A GTF file with the location (and details) about each adduct called by the pipepline

max_variants_2.DSC.vcf.gz : A VCF (Variant Call File) with information about mutations called.

coverage.rds : pre-computed coverage information in binary format to be loaded in R.

To analyze this data, use the following R files: adducts.R, mutations.R and jason-function-2022-04.R

The file "kallisto-h5.tar"  contains the output of running Kallisto on the regular RNAseq data (for expression level analysis). To analyze this data, use the following R files: Yeast-MNNG-MGT.Rmd and myDESeq2.R

The source code of the R files will need to be modified to point at the location of files on the computer being used. These modifications are pointed by comments in the code and are located towards the start of each file.