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# lift ikmc tracks from hg19 to hg38 (8/11/2015) 
# ceisenhart (Chris Eisenhart) 
    cd /hive/data/genomes/hg38/bed/hg19MassiveLift/ikmcGenes/README.txt
    hgsql hg19 -e "select * from hgIkmc" > IkmcGenes.bed
    cut -f 2,3,4,5,6,7,8,9,10,11,12,13 IkmcGenes.bed > hg19IkmcGenes.almostBed
    sed '1d' hg19IkmcGenes.almostbed > hg19IkmcGenesTrue.bed
    liftOver hg19IkmcGenesTrue.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz hg38IkmcGenes.bed unmapped.null
    hgLoadBed hg38 hgIkmc hg38IkmcGenes.bed
    hgsql hg19 -e "select * from hgIkmcExtra" > hgIkmcExtra.tab
    hgLoadSqlTab hg38 hgIkmcExtra $HOME/kent/src/hg/lib/genericAlias.sql hgIkmcExtra.tab
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# non-codingRNAs supertrack (DONE 08/19/2015 Chris Eisenhart) 
    # lincRNASeqReads (DONE 08/15/2015 Chris Eisenhart) 
	mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/nonCodingRNAs/lincRNASeqReads
	cd /hive/data/genomes/hg38/bed/hg19MassiveLift/nonCodingRNAs/lincRNASeqReads
	hgsql hg19 -e "show tables like 'lincRNA%' " > hg19lincRNATracksToBeLifted
	# Needs the shell script liftingScript and python liftAlotAtOnce 
	liftAlotAtOnce < hg19lincRNATracksToBeLifted
    ##############################################################################
    # lincRNATranscripts (DONE 08/15/2015 Chris Eisenhart) 
	mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/nonCodingRNAs/lincRNATranscripts
	cd /hive/data/genomes/hg38/bed/hg19MassiveLift/nonCodingRNAs/lincRNATranscripts
	# Needs the shell script liftingScript
	liftingScript lincRNAsTranscripts 
    ##############################################################################
    # wgRNA (DONE 04/13/2015 Chris Eisenhart) 
	mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/nonCodingRNAs/snoMiRNA
	cd /hive/data/genomes/hg38/bed/hg19MassiveLift/nonCodingRNAs/snoMiRNA
	# Needs the shell script liftingScript
	liftingScript wgRNA
##############################################################################
# wgEncodeReg ENCODE Regulatory tracks (Done Chris Eisenhart)
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg/wgEncodeRegMarkH3k27ac
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg/wgEncodeRegMarkH34me1
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg/wgEncodeRegMarkH3k4me3
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg/wgEncodeRegTfbsClusteredV3
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg/wgEncodeRegTxn
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/wgEncodeReg
    liftManyBigWigs /cluster/home/ceisenhart/kent/src/hg/utils/liftList/bigWigList.ra
##############################################################################
# coriellDelDup (DONE 08/24/2015 Chris Eisenhart) 
    mkdir /hive/data/genomes/hg38/bed/hg19MassiveLift/coriellDelDup
    cd /hive/data/genomes/hg38/bed/hg19MassiveLift/coriellDelDup
    hgsql hg19 -e "select * from coriellDelDup" | sed '1d' > coriellDelDup19.bed
    liftOver coriellDelDup19.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz coriellDelDup38.bed unmapped38.null -bedPlus=9 -tab
    hgLoadBed -tab -type=bed9+ -sqlTable=$HOME/kent/src/hg/lib/coriellDelDup.sql -as=$HOME/kent/src/hg/lib/coriellDelDup.as -bedDetail hg38 coriellDelDup coriellDelDup38.bed
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