Visualization/Summarize single molecule methylation profiles

[Chuang1118]

Hello,

My recent RNA004 direct RNA seq data (including two replicate samples) has done using the following: 1/ dorado basedcaller is aligned with transcript ID. 2/ Constructing bedMethyl tables by modkit pileup without reference. 3/ Detecting differential modification by modkit dmr pair

The result with the following position:

chrom	start	end
ENST00000006658	6	7
ENST00000006658	28	29
ENST00000006658	31	32
ENST00000006658	35	36
ENST00000006658	91	92
ENST00000006658	104	105
ENST00000006658	110	111
ENST00000006658	121	122
ENST00000006658	131	132

There are high intra-m6a heterogeneity within a single transcript. In other word, some sites are hyper-methylation and vice-versa. I converted manually the transcription coordinates to genomic coordinates to visualize in IGV see follow:

Zoom:

Is there a best way to visualize the sites found by dmr pair ? To summary, gene X in the KO sample has a high methylation percentage compared to the control sample.

Thank you, Chuang

[ArtRand]

Hello @Chuang1118,

Thanks for the question, and sorry for being slow to reply.

Normally (i.e. with DNA sequencing) I would recommend using the reads themselves in IGV (or any browser) as a qualitative visualization of the differences in base modification. Obviously this is more difficult when you align to the transcriptome, run DMR, then want to visualize on the genome. There are some tools that will perform the liftOver for you, but I don't have a recommended workflow on hand (I've asked my colleagues and will report back). Another option is to convert the DMR output into something that will create a visualization in IGV, something like adjusting the "color" field. Is this what you have in mind?