I start to look into the methodology of m6A-Seq data (from cDNA) and surprisingly find that it is quite similar to that of ChIP-Seq (from DNA) data analysis, which includes the main steps:
- fastq file processing
- mapping against genome
- narrow peak (summit)
- calling motif identification
- relating peaks to genes
I am wondering if there is any difference between the two types of sequencing in terms of data analysis I haven't noticed?
Is it possible to apply a standard ChIP-Seq analysis pipeline to m6A-Seq analysis?
Thanks a lot,