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 methylatuon 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