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# interactions track, May 2017 Max
also see the hg19.txt makeDoc ../hg19.txt for details

cd /hive/data/genomes/hg19/bed/interactions/

cd geneModels
# === hg38 ===

mysql hg38 -NBe 'select chrom, txStart, txEnd, name from wgEncodeGencodeBasicV26' > gencode26.bed
mysql hg38 -NBe 'select distinct name, name2 from wgEncodeGencodeBasicV26' > gencode26.names.tab
bedBestTranscript gencode26.bed gencode26.names.tab -m > gencode26.best.bed

# get best transcript for refGene
mysql hg38 -NBe 'select chrom, txStart, txEnd, name from refGene' > refGene-hg38.bed
mysql hg38 -NBe 'select distinct name, name2 from refGene' > refGene-hg38.names.tab
bedBestTranscript refGene-hg38.bed refGene-hg38.names.tab -m > refGene-hg38.best.bed

# add all gencode comprehensive models, but only as a last resort
mysql hg38 -NBe 'select chrom, txStart, txEnd, name from wgEncodeGencodeCompV26' > gencodeComp26.bed
mysql hg38 -NBe 'select distinct name, name2 from wgEncodeGencodeCompV26' > gencodeComp26.names.tab
bedBestTranscript -m gencodeComp26.bed gencodeComp26.names.tab > gencodeComp26.best.bed

bedNamePickFirst gencode26.best.bed refGene-hg38.best.bed gencodeComp26.best.bed | cut -f-4 | bedSort stdin stdout > bestGenes.hg38.bed 
== END GENE MODELS ==
ggTables bigBed mysql/ bigBed/ geneModels/bestGenes.hg38.bed hg38
ln -s `pwd`/bigBed/geneInteractions.hg38.bb /gbdb/hg38/bbi/interactions.bb