Annotating my DMRs for all pairwise comparisons for genomic features.

In [7]: 
!cd /Users/Shared/Apps/bedtools-2.17.0/bin
In [9]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M1M3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM1M3.txt
In [10]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M1T1D3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM1T1D3.txt
In [11]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M1T1D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM1T1D5.txt
In [12]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M1T3D3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM1T3D3.txt
In [13]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M1T3D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM1T3D5.txt
In [14]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M3T1D3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM3T1D3.txt
In [15]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M3T1D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM3T1D5.txt
In [16]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M3T3D3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM3T3D3.txt
In [17]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/M3T3D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedM3T3D5.txt
In [18]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/T1D3T1D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedT1D3T1D5.txt
In [19]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/T1D3T3D3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedT1D3T3D3.txt
In [20]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/T1D3T3D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedT1D3T3D5.txt
In [21]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/T1D5T3D3.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedT1D5T3D3.txt
In [22]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/T1D5T3D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedT1D5T3D5.txt
In [23]: 
!intersectBed -a /Volumes/web/Mollusk/Crassostrea_gigas.GCA_000297895.1.22.gff3 -b /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/T3D3T3D5.bed > /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/bedtools_DMRs/annotatedT3D3T3D5.txt
In [1]: 
#NOTEBOOK NAME
nb='DMR_annotation_genefeatures'

#NOTEBOOK LOCATION
nbloc='/Users/claireolson/Dropbox/Lab\ \(1\)/IPython_nbs/Claire/'



#TIMESTAMP
date=!date +%m%d_%H%M
#LOCATION OF POST DIRECTORY
post='/Volumes/web/Mollusk/iPython_Posts/'
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