Posted by & filed under Cgigas DNA Methylation.

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


Jupyter Notebook

Could also do this on a less conservative approach by acting on (sig) tracks in bedtools