8a88f3d9cb80250c8449e028052898b824a1599d
max
  Mon May 12 05:23:50 2025 -0700
adding HAQers to unusual cons track, suggested by Katie Pollard, refs #35703

diff --git src/hg/makeDb/doc/hg38/unusualcons.txt src/hg/makeDb/doc/hg38/unusualcons.txt
index a2851d4efb4..06058afbc34 100644
--- src/hg/makeDb/doc/hg38/unusualcons.txt
+++ src/hg/makeDb/doc/hg38/unusualcons.txt
@@ -1,47 +1,51 @@
 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