Modalysis: DNA Methylation Analysis from Long Read Oxford-Nanopore Sequencing Data

Arnav Bharti, Priyanka Roy, Tanmaya Mahapatra, Sanjay Kumar Kochar, Dhanpat Kumar Kochar, and Ashis Das

Product Demo

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Documentation

Access full project documentation at Modalysis.arnavbharti.com.

Sample Output Files (TSV)

methylation_summary.tsv

sample_id	chromosome	total_sites	methylated_sites	methylation_percent
S1	chr1	12540	5830	46.49
S1	chr2	11892	5491	46.17
S1	chr3	13011	6110	46.96

gene_level_signal.tsv

gene_id	gene_name	mean_methylation	read_count	coverage
PF3D7_0100100	msp1	0.42	521	38.4
PF3D7_0202000	ama1	0.57	489	34.1
PF3D7_0304600	csp	0.36	442	29.7

region_calls.tsv

region_id	chromosome	start	end	call	confidence
R001	chr1	10500	11250	Hypomethylated	0.91
R002	chr2	20440	21380	Hypermethylated	0.87
R003	chr3	9900	10810	Intermediate	0.79

qc_metrics.tsv

sample_id	mean_read_length	mapped_reads	mapping_rate	duplication_rate
S1	12874	1452300	0.964	0.071
S2	11992	1394421	0.957	0.076
S3	13201	1528432	0.971	0.068

differential_sites.tsv

site_id	chromosome	position	group_a_beta	group_b_beta	delta_beta	p_value
DS001	chr1	11041	0.44	0.62	0.18	0.0021
DS002	chr2	20975	0.52	0.33	-0.19	0.0014
DS003	chr3	10112	0.38	0.55	0.17	0.0039