hg38-radar-hg38
RADAR RNA editing events: (http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt) installs a BED file of the RADAR events, preconverted to hg38 how this file was created: 1. Download the hg19 RADAR file and converted to BED format. url=http://www.stanford.edu/~gokulr/database/Human_AG_all_hg19_v2.txt mkdir -p editing cd editing wget -qO- $url | awk 'BEGIN{OFS="\t"} {print $1,$2,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11}' | sed "s/position position/start end/" > RADAR-hg19.bed cd ../ 2. Convert RADAR BED file to BED3 format. cut -f1,2,3 RADAR-hg19.bed > RADAR-hg19.tmp.bed 3. Get the Crossmap hg19 to hg38 chain file: wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz 4. Run Crossmap: Crossmap.py bed hg19ToHg38.over.chain.gz RADAR-hg19.tmp.bed > conversions.bed 5. Merge original RADAR file with the Crossmap output wget https://raw.githubusercontent.com/roryk/seqscripts/master/radar-convert-annotations.py python radar-convert-annotations.py RADAR-hg19.bed conversions.bed RADAR-hg38.bed.gz