The m6A-Seq analysis

Question

[wangdp123]

Hi there,

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,

Tom

Answer 1

[ZZzzzzhong]

It's not very exactly to apply s standard Chip-Seq analysis pipeline to m6A-Seq analysis.RNA' expression is dynamic.So the distribution model is different with chipseq'data(exomePeak is designed to call peaks of m6A seq).m6Aseq belong to RNA which involves the splicing site, it's best to use RNA alignment tools(such as hisat2)