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