Side track with tracks

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

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