a442752cfb1738add6158966133902bdc47e69d0
max
  Sun May 25 14:11:39 2025 -0700
adding ucnebase to unusual conservation track, refs #35703

diff --git src/hg/makeDb/doc/hg38/unusualcons.txt src/hg/makeDb/doc/hg38/unusualcons.txt
index 06058afbc34..53447754467 100644
--- src/hg/makeDb/doc/hg38/unusualcons.txt
+++ src/hg/makeDb/doc/hg38/unusualcons.txt
@@ -1,51 +1,63 @@
 mkdir /hive/data/genomes/hg38/bed/unusualcons/
 
 mkdir /hive/data/genomes/hg38/bed/unusualcons/hars/
 mkdir hg19
 cd hg19
 wget https://docpollard.org/wordpress/wp-content/research/nchaes_merged_hg19.bed
 cd ../
 mkdir hg38
 cd hg38
 liftOver ../hg19/nchaes_merged_hg19.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz  ../hg38/nchaes_merged_hg38.bed unmapped.txt
 bedSort nchaes_merged_hg38.bed  nchaes_merged_hg38.bed
 bedToBigBed nchaes_merged_hg38.bed ../../../../chrom.sizes nchaes_merged_hg38.bb
 # downloaded Excel table from pollard lab homepage and converted to text using Excel
 cut -f1,2,3,4 -d'	' KeoughTableS1.txt | grep -v ^chrom | grep -v ^positive > KeoughTableS1.bed
 bedSort KeoughTableS1.bed KeoughTableS1.bed
 bedToBigBed KeoughTableS1.bed ../../../chrom.sizes KeoughTableS1.bb
 
 mkdir /hive/data/genomes/hg38/bed/unusualcons/hcondels/
 cd /hive/data/genomes/hg38/bed/unusualcons/hcondels/
 # from science.abn2253_tables_s1_to_s4.xls created three text files
 paste meta.txt mpradeseq.txt > both.txt
 ~/kent/src/utils/tabToBed/tabToBed both.txt hcondels.bed hcondels.as --bedFields=chrom=hg38_mpra_chr,start=hg38_mpra_start_pos,end=hg38_mpra_end_pos,name=hCONDEL_ID
 bedToBigBed hcondels.bed /hive/data/genomes/hg38/chrom.sizes hcondels.bb -tab -type=bed12+ -as=hcondels.as
 
 mkdir /hive/data/genomes/hg38/bed/unusualcons/longhcondels/
 cd /hive/data/genomes/hg38/bed/unusualcons/longhcondels/
 # converted manually excel Excel in supp2 in https://pmc.ncbi.nlm.nih.gov/articles/PMC3071156/#S2
 # fix position mistakes
 cat supp2.hg18.bed | tawk '{if ($3<$2) { t=$2; $2=$3; $3=t }; print } ' | less > supp2.hg18.fixed.bed
 # lift to hg38
 liftOver supp2.hg18.fixed.bed /hive/data/genomes/hg18/bed/liftOver/hg18ToHg38.over.chain.gz supp2.hg38.bed unmapped.txt
 # convert
 bedSort supp2.hg38.bed supp2.hg38.bed
 bedToBigBed supp2.hg38.bed ../../../chrom.sizes hcondels583.bb
 
 mkdir /hive/data/genomes/hg38/bed/unusualcons/ultras/
 cd /hive/data/genomes/hg38/bed/unusualcons/ultras/
 wget http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hg19/hg19.ultraConserved.bb
 bigBedToBed hg19.ultraConserved.bb hg19.ultraConserved.bed
 liftOver hg19.ultraConserved.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz hg38.ultraConserved.bed unmapped.txt
 bedToBigBed hg38.ultraConserved.bed ../../../chrom.sizes hg38.ultraConserved.bb
 
 mkdir /hive/data/genomes/hg38/bed/unusualcons/zooUces/
 cd /hive/data/genomes/hg38/bed/unusualcons/zooUces/
 wget https://cgl.gi.ucsc.edu/data/cactus/zoonomia-2021-track-hub/hg38/zooUCEs.bed.gz
 wget https://cgl.gi.ucsc.edu/data/cactus/zoonomia-2021-track-hub/hg38/RoCCs.bigBed
 wget https://cgl.gi.ucsc.edu/data/cactus/zoonomia-2021-track-hub/hg38/UNICORNs.bigBed
 
 cd /hive/data/genomes/hg38/bed/unusualcons/haqers/
 bedSort haqers.bed haqers.bed 
 bedToBigBed haqers.bed ../../../chrom.sizes haqers.bb
+
+# UCNEbase
+mkdir /hive/data/genomes/hg38/bed/unusualcons/ucnebase/hg19
+cd /hive/data/genomes/hg38/bed/unusualcons/ucnebase/hg19
+wget https://epd.expasy.org/ucnebase/data/UCNEs_hg19.bed
+# split file manually in vim
+mkdir /hive/data/genomes/hg38/bed/unusualcons/ucnebase/hg38
+cd /hive/data/genomes/hg38/bed/unusualcons/ucnebase/hg38
+liftOver ../hg19/chicken.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz  chicken.hg38.bed unmapped.txt
+liftOver ../hg19/clusters.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz  clusters.bed unmapped.txt
+liftOver ../hg19/paralogs.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz  paralogs.bed unmapped.txt
+for i in *.bed; do bedSort $i $i; bedToBigBed $i ../../../../chrom.sizes `basename $i .bed`.bb; done