Get in Control - Cv multiomics

In an effort to couple DNA methylation data to complementary RNA-seq data we are looking at what the DNA methylation landscape, DML look like. Oysters were exposed to ocean acidification. Males and females were included.

TLDR- Sex related methylation differences are FAR greater than any OA associated methylation differences.

Sample information

Sample.ID	OldSample.ID	Treatment	Sex	TreatmentN	Parent.ID
12M	S12M	Exposed	M	3	EM05
13M	S13M	Control	M	1	CM04
16F	S16F	Control	F	2	CF05
19F	S19F	Control	F	2	CF08
22F	S22F	Exposed	F	4	EF02
23M	S23M	Exposed	M	3	EM04
29F	S29F	Exposed	F	4	EF07
31M	S31M	Exposed	M	3	EM06
35F	S35F	Exposed	F	4	EF08
36F	S36F	Exposed	F	4	EF05
39F	S39F	Control	F	2	CF06
3F	S3F	Exposed	F	4	EF06
41F	S41F	Exposed	F	4	EF03
44F	S44F	Control	F	2	CF03
48M	S48M	Exposed	M	3	EM03
50F	S50F	Exposed	F	4	EF01
52F	S52F	Control	F	2	CF07
53F	S53F	Control	F	2	CF02
54F	S54F	Control	F	2	CF01
59M	S59M	Exposed	M	3	EM01
64M	S64M	Control	M	1	CM05
6M	S6M	Control	M	1	CM02
76F	S76F	Control	F	2	CF04
77F	S77F	Exposed	F	4	EF04
7M	S7M	Control	M	1	CM01
9M	S9M	Exposed	M	3	EM02

Looking just at controls

file.list_c=list('../bg_data/13M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/16F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/39F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/44F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/52F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/53F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/54F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/64M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/6M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/76F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/7M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam'
)

myobj_c = processBismarkAln(location = file.list_c,
  sample.id = list("13M","16F","19F","39F","44F","52F","53F","54F", "64M", "6M", "76F", "7M"),
  assembly = "cv",
  read.context="CpG",
  mincov=2,
  treatment = c(0,1,1,1,1,1,1,1,0,0,1,0))

filtered.myobj=filterByCoverage(myobj_c,lo.count=10,lo.perc=NULL,
                                      hi.count=NULL,hi.perc=98)

meth_filter=unite(filtered.myobj, min.per.group=NULL, destrand=TRUE)

clusterSamples(meth_filter, dist="correlation", method="ward", plot=TRUE)

PCASamples(meth_filter)

con

and when one includes

all samples

all

note different file list

file.list_all=list('../bg_data/12M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/13M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/16F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/19F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/22F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/23M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/29F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/31M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/35F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/36F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/39F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/3F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/41F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/44F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/48M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/50F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/52F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/53F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/54F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/59M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/64M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/6M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/76F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/77F_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/7M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam',
                '../bg_data/9M_R1_val_1_bismark_bt2_pe.deduplicated.sorted.bam'
)

and align

myobj_all = processBismarkAln(location = file.list_all,
  sample.id = list("12M","13M","16F","19F","22F","23M","29F","31M", "35F","36F","39F","3F","41F","44F","48M","50F","52F","53F","54F","59M","64M","6M","76F", "77F","7M","9M"),
  assembly = "cv",
  read.context="CpG",
  mincov=2,
  treatment = c(3,1,2,2,4,3,4,3,4,4,2,4,4,2,3,4,2,2,2,3,1,1,2,4,1,3))

Written on November 3, 2021