MethylExtract

 

Guillermo Barturen, Antonio Rueda, José L. Oliver and Michael Hackenberg
MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
How to cite

For questions and feedback, please contact to: MH - mlhack@gmail.com, GB - bartg01@gmail.com, RL - rlebron@ugr.es

 

FAQs

  • Does MethylExtract extract a list of SNVs?
  • Yes, no matter the methylation context selected. MethylExtract will retrieve a VCF file with all the SNVs detected on the bisulfite treated sample.

  • Can MethylExtract manage BAM files?
  • Yes, but remember that samtools must be installed

  • Can MethylExtract remove duplicates from pair-end reads?
  • MethylExtract removes duplicates from pair-end reads as they were single-end. For the moment we recommend the users to remove pair-end duplicates using samtools or picards.

  • How can be extracted the reads from the unmethylated chromosome to run MethylExtractBSCR?
  • Please check section 5 on the manual, detailed instructions had been added.

  • How can be extracted the fasta sequence from the unmethylated chromosome from a multifasta file?
  • Please check section 5 on the manual, detailed instructions had been added.



© Computational Genomics and Bioinformatics Group
Dept. of Genetics & Inst. of Biotechnology
University of Granada, Spain