In [1]:

#deleting first row of text file
!tail -n +2 /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethylatedCGs_oysterv9.txt > /Users/claireellis/Desktop/MethylatedCGs_oysterv9_tail.txt

In [2]:

!head /Users/claireellis/Desktop/MethylatedCGs_oysterv9_tail.txt

C10093	methratio	CpG	107	108	1	+	.	.

C10137	methratio	CpG	18	19	0.733	+	.	.

C10137	methratio	CpG	30	31	0.778	+	.	.

C10137	methratio	CpG	39	40	0.783	+	.	.

C10137	methratio	CpG	72	73	0.524	+	.	.

C10137	methratio	CpG	81	82	0.692	+	.	.

C10137	methratio	CpG	97	98	0.556	+	.	.

C10311	methratio	CpG	56	57	1	+	.	.

C10671	methratio	CpG	22	23	0.5	+	.	.

C10671	methratio	CpG	152	153	0.5	+	.	.

In [4]:

!intersectBed -a /Users/claireellis/Desktop/MethylatedCGs_oysterv9_tail.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Exons_v9_CGs.txt > /Users/claireellis/Desktop/MethylatedCGs_Exons.txt

In [5]:

#this is the command to get line counts for EXONS
!wc /Users/claireellis/Desktop/MethylatedCGs_Exons.txt

  343032 3087288 17692941 /Users/claireellis/Desktop/MethylatedCGs_Exons.txt

In [6]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/ModeratelyMethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Exons_v9_CGs.txt > /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Exons.txt

In [7]:

!wc /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Exons.txt

   61839  556551 3248011 /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Exons.txt

In [8]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/UnmethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Exons_v9_CGs.txt > /Users/claireellis/Desktop/UnmethylatedCGs_Exons.txt

In [9]:

!wc /Users/claireellis/Desktop/UnmethylatedCGs_Exons.txt

  623331 5609979 30450276 /Users/claireellis/Desktop/UnmethylatedCGs_Exons.txt

In [11]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Introns_v9_CGs.txt > /Users/claireellis/Desktop/MethylatedCGs_Introns.txt

In [12]:

!wc /Users/claireellis/Desktop/MethylatedCGs_Introns.txt

  518734 4668606 26896216 /Users/claireellis/Desktop/MethylatedCGs_Introns.txt

In [13]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/ModeratelyMethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Introns_v9_CGs.txt > /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Introns.txt

In [14]:

!wc /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Introns.txt

  287921 2591289 15149108 /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Introns.txt

In [15]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/UnmethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Introns_v9_CGs.txt > /Users/claireellis/Desktop/UnmethylatedCGs_Introns.txt

In [16]:

!wc /Users/claireellis/Desktop/UnmethylatedCGs_Introns.txt

 1493130 13438170 72967782 /Users/claireellis/Desktop/UnmethylatedCGs_Introns.txt

In [17]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/TEs_v9_CGs.txt > /Users/claireellis/Desktop/MethylatedCGs_TEs.txt

In [18]:

!wc /Users/claireellis/Desktop/MethylatedCGs_TEs.txt

   38532  346788 1994156 /Users/claireellis/Desktop/MethylatedCGs_TEs.txt

In [19]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/ModeratelyMethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/TEs_v9_CGs.txt > /Users/claireellis/Desktop/ModeratelyMethylatedCGs_TEs.txt

In [20]:

!wc /Users/claireellis/Desktop/ModeratelyMethylatedCGs_TEs.txt

  120699 1086291 6316822 /Users/claireellis/Desktop/ModeratelyMethylatedCGs_TEs.txt

In [21]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/UnmethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/TEs_v9_CGs.txt > /Users/claireellis/Desktop/UnmethylatedCGs_TEs.txt

In [22]:

!wc /Users/claireellis/Desktop/UnmethylatedCGs_TEs.txt

  395065 3555585 19189051 /Users/claireellis/Desktop/UnmethylatedCGs_TEs.txt

In [23]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Promoter_v9_CGs.txt > /Users/claireellis/Desktop/MethylatedCGs_Promoter.txt

In [24]:

!wc /Users/claireellis/Desktop/MethylatedCGs_Promoter.txt

   45241  407169 2336384 /Users/claireellis/Desktop/MethylatedCGs_Promoter.txt

In [25]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/ModeratelyMethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Promoter_v9_CGs.txt > /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Promoter.txt

In [26]:

!wc /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Promoter.txt

   46353  417177 2428131 /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Promoter.txt

In [27]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/UnmethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Promoter_v9_CGs.txt > /Users/claireellis/Desktop/UnmethylatedCGs_Promoter.txt

In [29]:

!wc /Users/claireellis/Desktop/UnmethylatedCGs_Promoter.txt

  401809 3616281 19600390 /Users/claireellis/Desktop/UnmethylatedCGs_Promoter.txt

In [30]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Other_v9_CGs.txt > /Users/claireellis/Desktop/MethylatedCGs_Other.txt

In [31]:

!wc /Users/claireellis/Desktop/MethylatedCGs_Other.txt

  277587 2498283 14287492 /Users/claireellis/Desktop/MethylatedCGs_Other.txt

In [32]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/ModeratelyMethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Other_v9_CGs.txt > /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Other.txt

In [33]:

!wc /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Other.txt

  523351 4710159 27221753 /Users/claireellis/Desktop/ModeratelyMethylatedCGs_Other.txt

In [34]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/UnmethylatedCGs_oysterv9.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Other_v9_CGs.txt > /Users/claireellis/Desktop/UnmethylatedCGs_Other.txt

In [35]:

!wc /Users/claireellis/Desktop/UnmethylatedCGs_Other.txt

 2911842 26206578 141309194 /Users/claireellis/Desktop/UnmethylatedCGs_Other.txt

In [36]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethandUnmeth_Over5xCoverage.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Exons_v9_CGs.txt > /Users/claireellis/Desktop/MethandUnmethCGs_Exons.txt

In [37]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethandUnmeth_Over5xCoverage.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Introns_v9_CGs.txt > /Users/claireellis/Desktop/MethandUnmethCGs_Introns.txt

In [38]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethandUnmeth_Over5xCoverage.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/TEs_v9_CGs.txt > /Users/claireellis/Desktop/MethandUnmethCGs_TEs.txt

In [39]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethandUnmeth_Over5xCoverage.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Promoter_v9_CGs.txt > /Users/claireellis/Desktop/MethandUnmethCGs_Promoter.txt

In [40]:

!intersectBed -a /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Methylated_Unmethylated_Files/MethandUnmeth_Over5xCoverage.txt -b /Volumes/web-1/Mollusk/174gm_analysis/Whole_Genome_Analyses/intersectBedfiles_StevensTracks/Other_v9_CGs.txt > /Users/claireellis/Desktop/MethandUnmethCGs_Other.txt

In []:

#code for R density plot for manuscript:

CDS<-read.delim("~/Desktop/MethandUnmethCGs_Exons.txt", header = TRUE, sep = "\t")
d<-density(CDS$score)
plot(d, xlab= "Proportion Methylation", ylim=c(0,10), col="red", lwd=2)

Introns<-read.delim("~/Desktop/MethandUnmethCGs_Introns.txt", header= TRUE, sep = "\t")
e<-density(Introns$score)
lines(e, xlab="Proportion Methylation", col="blue", lwd=2)

Promoter<-read.delim("~/Desktop/MethandUnmethCGs_Promoter.txt", header= TRUE, sep = "\t")
f<-density(Promoter$score)
lines(f, xlab="Proportion Methylation", col="darkgreen", lwd=2)

TEs<-read.delim("~/Desktop/MethandUnmethCGs_TEs.txt", header= TRUE, sep = "\t")
g<-density(TEs$score)
lines(g, xlab="Proportion Methylation", col="darkorange", lwd=2)