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
@@ -37,15 +37,27 @@
 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