Ive been reading the Lux documentation, which is a quantifier of 5mc and 5hmc and they say the input files for this program are the converted and non converted counts extracted and generated with bismark , and then a python script has to convert those files into lux-compatible files.
MY QUESTION: In which step of bismark do i get the converted and non converted counts files? Is it just after alignment? or after methylation extraction? (My guess is methylation extraction in bismark only extracts BS-Seq information (5mC) so the files I need should be generated before this step).
Here are the literal instructions of the pipeline:
An usual lux pipeline has the following steps:
- Alignment of BS-seq and oxBS-seq data (e.g. bismark or bsmooth)
- Extraction of converted and unconverted counts (e.g. bismark or bsmooth)
- Generation of input afiles for lux parse.py)
- Integrativ emethylation analysis (lux)
- Calculation of Bayes factorsbf.py)
This documentation only focuses on points 3,4 and 5.
Thank you in advance