Question about the data source for Bacmethy.

LiuJih2021 / Bacmethy

Bacmethy, a customizable pipeline based on Docker, reliably calculates the enrichment significance of methylated and un(der)methylated motifs in regulatory and coding regions of the genome

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Question about the data source for Bacmethy. #2

Open OtaviaW opened 7 months ago

OtaviaW commented 7 months ago

Hi there, it is a great work of Bacmethy. I'd like to know if Bacmethy only supports Single Molecule Real-Time（SMRT）Sequencing data or it is compatible with Illuminasequencing data ?

LiuJih2021 commented 7 months ago

Thank you for your appreciation of Bacmethy. Bacmethy relies on the methylation signals at genomic sites for identification. If the chromosome IDs in your methylation files, which are found in the first column of your GFF files(motifs.gff), match the IDs used in your Illumina sequencing data(genome.fasta), it is technically possible to use the data. However, I recommend using data directly from SMRT sequencing for analysis rather than mixing different data types, as this might lead to errors.