Lux oxBS-seq and BS-seq quantificator of 5mc and 5hmC. Which are the input files?
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3.9 years ago
Pin.Bioinf ▴ 300

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:

  1. Alignment of BS-seq and oxBS-seq data (e.g. bismark or bsmooth)
  2. Extraction of converted and unconverted counts (e.g. bismark or bsmooth)
  3. Generation of input afiles for lux parse.py)
  4. Integrativ emethylation analysis (lux)
  5. Calculation of Bayes factorsbf.py)

This documentation only focuses on points 3,4 and 5.

Thank you in advance

bs-seq bisulfite bismark lux • 732 views
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