Today working on our paper looking at heat stress and DNA methylation I dived deeper into the array data in the search for what should be called a DMR.
As a refresher we have tracks from the core that have 1.8+ fold difference (sig) and complementary tracks where there are three adjacents (3plusAdjacent). I made tracks where I merged the latter into a single feature when within 100bp of each other.
In order to see if there is any consistency across oysters..
#concatenated tracks
!cat \
/Volumes/web/halfshell/2015-05-comgenbro/2M_3plusmerge_Hypo.bed \
/Volumes/web/halfshell/2015-05-comgenbro/4M_3plusmerge_Hypo.bed \
/Volumes/web/halfshell/2015-05-comgenbro/6M_3plusmerge_Hypo.bed \
> /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed
#then using bedtools merge features (though first had to sort)
!bedtools sort -i /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed \
> /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcatsort.bed
!bedtools merge -c 2 -o count \
-i /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcatsort.bed | sort -nrk4
and so on for the hypermethylated region.
end of the AM, left with a new track
scaffold481 576986 578532 -3 scaffold247 141885 142442 -3 scaffold1518 212680 213736 -3 scaffold853 46186 46496 -2 scaffold406 419330 419384 -2 scaffold406 419005 419060 -2 scaffold406 418360 418767 -2 scaffold394 555813 556224 -2 scaffold247 144031 144583 -2 scaffold242 75918 76344 -2 scaffold142 656144 656735 -2 scaffold12 243960 244376 -2 scaffold257 1235165 1235481 +2
Could also do this on a less conservative approach by acting on (sig) tracks in bedtools
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