Skip to content

methbase

Directory actions

More options

Directory actions

More options

Latest commit

 

History

History

methbase

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
methbase.run.sh
methbase.run.sh
 
 
readme.md
readme.md
 
 

readme.md

Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease

Human_B_Lymphocyte

wget http://smithdata.usc.edu/methbase/data/Ball-Human-2009/Human_BLymphocyte/tracks_hg19/Human_BLymphocyte.meth.bw -O  Human_BALL_Ball_Human-2009.meth.bw
wget http://smithdata.usc.edu/methbase/data/Lee-Human-2015/Human_BALLhyperdiploid/tracks_hg19/Human_BALLhyperdiploid.meth.bw -O Human_BALL_hyperdiploid_Lee-Human-2015.meth.bw
wget http://smithdata.usc.edu/methbase/data/Lee-Human-2015/Human_BALLETV6RUNX1/tracks_hg19/Human_BALLETV6RUNX1.meth.bw -O Human_BALL_ETV6RUNX1-Human-2015.meth.bw
cat  Human_BALL_*.wig > HUman_BALL_WGBS.wig
grep -v '#' HUman_BALL_WGBS.wig > HUman_BALL_WGBS.wig.bed
perl wigAverage.pl HUman_BALL_WGBS.wig.bed > HUman_BALL_WGBS.wig.bed.uni
bedtools sort -i HUman_BALL_WGBS.wig.bed.uni > HUman_BALL_WGBS.wig.bed.uni.sort
echo 'track type=bedGraph name="AML" description="AML" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > HUman_BALL_WGBS.wig.bed.uni.sort.UCSC
cat  HUman_BALL_WGBS.wig.bed.uni.sort >> HUman_BALL_WGBS.wig.bed.uni.sort.UCSC
head HUman_BALL_WGBS.wig.bed.uni.sort.UCSC
gzip HUman_BALL_WGBS.wig.bed.uni.sort.UCSC

AML

wget http://smithdata.usc.edu/methbase/data/Akalin-Human-2012/Human_AML/tracks_hg19/Human_AML.meth.bw -O Human_AML_Akalin-Human-2012.meth.bw
wget http://smithdata.usc.edu/methbase/data/Lund-Human-2014/Human_AML3-Control/tracks_hg19/Human_AML3-Control.meth.bw -O Human_AML3_Lund-Human-2014.meth.bw
cat  Human_AML*.wig > HUman_AML_WGBS.wig
grep -v '#' HUman_AML_WGBS.wig > HUman_AML_WGBS.wig.bed
perl wigAverage.pl HUman_AML_WGBS.wig.bed > HUman_AML_WGBS.wig.bed.uni
bedtools sort -i HUman_AML_WGBS.wig.bed.uni > HUman_AML_WGBS.wig.bed.uni.sort
echo 'track type=bedGraph name="AML" description="AML" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > HUman_AML_WGBS.wig.bed.uni.sort.UCSC
cat  HUman_AML_WGBS.wig.bed.uni.sort >> HUman_AML_WGBS.wig.bed.uni.sort.UCSC
head HUman_AML_WGBS.wig.bed.uni.sort.UCSC
gzip HUman_AML_WGBS.wig.bed.uni.sort.UCSC

Normal pancrease and pancreatic cancer

for i in {1..12}
do
wget http://smithdata.usc.edu/methbase/data/Thompson-Human-2015/Human_PancreaticCancer$i/tracks_hg19/Human_PancreaticCancer$i.meth.bw &
done
wget http://smithdata.usc.edu/methbase/data/Thompson-Human-2015/Human_NormalPancreas1/tracks_hg19/Human_NormalPancreas1.meth.bw
wget http://smithdata.usc.edu/methbase/data/Thompson-Human-2015/Human_NormalPancreas2/tracks_hg19/Human_NormalPancreas2.meth.bw

cat *_PancreaticCancer*.wig > PANcreaticCancer.wig
grep -v '#' PANcreaticCancer.wig > PANcreaticCancer.wig.bed
perl wigAverage.pl PANcreaticCancer.wig.bed > PANcreaticCancer.wig.bed.uni
bedtools sort -i PANcreaticCancer.wig.bed.uni > PANcreaticCancer.wig.bed.uni.sort
echo 'track type=bedGraph name="PancreaticCancer" description="_PancreaticCancer" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > PANcreaticCancer.wig.bed.uni.sort.UCSC
cat  PANcreaticCancer.wig.bed.uni.sort >> PANcreaticCancer.wig.bed.uni.sort.UCSC
head PANcreaticCancer.wig.bed.uni.sort.UCSC
gzip PANcreaticCancer.wig.bed.uni.sort.UCSC

cat *_NormalPancreas*.wig > NormalPancreas.wig
grep -v '#' NormalPancreas.wig > NormalPancreas.wig.bed
perl wigAverage.pl NormalPancreas.wig.bed > NormalPancreas.wig.bed.uni
bedtools sort -i NormalPancreas.wig.bed.uni > NormalPancreas.wig.bed.uni.sort
echo 'track type=bedGraph name="PancreaticCancer" description="_PancreaticCancer" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > PANcreaticCancer.wig.bed.uni.sort.UCSC
cat  PANcreaticCancer.wig.bed.uni.sort >> PANcreaticCancer.wig.bed.uni.sort.UCSC
head PANcreaticCancer.wig.bed.uni.sort.UCSC
gzip PANcreaticCancer.wig.bed.uni.sort.UCSC

PBMC

wget http://smithdata.usc.edu/methbase/data/Li-PBMC-2010/Human_PBMC/tracks_hg19/Human_PBMC.meth.bw -O Human_PBMC_Li2010.bw &
wget http://smithdata.usc.edu/methbase/data/Heyn-Human-NewbornCentenarian-2012/Human_PBMC/tracks_hg19/Human_PBMC.meth.bw -O Human_PBMC_Heyn2012.meth.bw &
wget http://smithdata.usc.edu/methbase/data/Heyn-Human-NewbornCentenarian-2012/Human_CD4T-100yr/tracks_hg19/Human_CD4T-100yr.meth.bw -O Human_CD4T-100yr.meth.bw
wget http://smithdata.usc.edu/methbase/data/Heyn-Human-NewbornCentenarian-2012/Human_CD4T-Newborn/tracks_hg19/Human_CD4T-Newborn.meth.bw -O 
wget http://smithdata.usc.edu/methbase/data/Pacis-Human-2015/Human_DendriticCell/tracks_hg19/Human_DendriticCell.meth.bw -O Human_DendriticCell_hg19.meth.bw

cat Human_PBMC_*wig > HUman_PBMC_hg19.wig
grep -v '#' HUman_PBMC_hg19.wig > HUman_PBMC_hg19.wig.bed
perl wigAverage.pl HUman_PBMC_hg19.wig.bed > HUman_PBMC_hg19.wig.bed.uni
bedtools sort -i HUman_PBMC_hg19.wig.bed.uni > HUman_PBMC_hg19.wig.bed.uni.sort
echo 'track type=bedGraph name="PBMC" description="PBMC" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > HUman_PBMC_hg19.wig.bed.uni.sort.UCSC
cat  HUman_PBMC_hg19.wig.bed.uni.sort >> HUman_PBMC_hg19.wig.bed.uni.sort.UCSC
head HUman_PBMC_hg19.wig.bed.uni.sort.UCSC
gzip HUman_PBMC_hg19.wig.bed.uni.sort.UCSC

cat Human_CD4T*wig > HUman_CD4T_hg19.wig
grep -v '#' HUman_CD4T_hg19.wig > HUman_CD4T_hg19.wig.bed
perl wigAverage.pl HUman_CD4T_hg19.wig.bed > HUman_CD4T_hg19.wig.bed.uni
bedtools sort -i HUman_CD4T_hg19.wig.bed.uni > HUman_CD4T_hg19.wig.bed.uni.sort
echo 'track type=bedGraph name="CD4+" description="CD4+" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > HUman_CD4T_hg19.wig.bed.uni.sort.UCSC
cat  HUman_CD4T_hg19.wig.bed.uni.sort >> HUman_CD4T_hg19.wig.bed.uni.sort.UCSC
head HUman_CD4T_hg19.wig.bed.uni.sort.UCSC
gzip -f HUman_CD4T_hg19.wig.bed.uni.sort.UCSC

SID="HUman_B_Cell_hg19"
cat Human_BCell*wig > $SID.wig
grep -v '#' $SID.wig > $SID.wig.bed
perl wigAverage.pl $SID.wig.bed > $SID.wig.bed.uni
bedtools sort -i $SID.wig.bed.uni > $SID.wig.bed.uni.sort
echo 'track type=bedGraph name="Human_B_Cell" description="Human_B_Cell" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > $SID.wig.bed.uni.sort.UCSC
cat  $SID.wig.bed.uni.sort >> $SID.wig.bed.uni.sort.UCSC
head $SID.wig.bed.uni.sort.UCSC
gzip -f $SID.wig.bed.uni.sort.UCSC

SID="Human_Neutrophil_hg19"
cat Human_Neut*bw.wig > $SID.wig
grep -v '#' $SID.wig > $SID.wig.bed
perl wigAverage.pl $SID.wig.bed > $SID.wig.bed.uni
bedtools sort -i $SID.wig.bed.uni > $SID.wig.bed.uni.sort
echo 'track type=bedGraph name="Human_Neutrophil" description="Human_Neutrophil" visibility=full color=227,207,87 altColor=200,100,0 priority=20 maxHeightPixels=128:64:32 visibility=full' > $SID.wig.bed.uni.sort.UCSC
cat  $SID.wig.bed.uni.sort >> $SID.wig.bed.uni.sort.UCSC
head $SID.wig.bed.uni.sort.UCSC
gzip -f $SID.wig.bed.uni.sort.UCSC