5b9c29a85bcda6fde942cfa0622172c9b8355ac2 max Tue May 6 07:58:45 2025 -0700 adding makedoc for unusual conservation track, refs #35703 diff --git src/hg/makeDb/doc/hg38/unusualcons.txt src/hg/makeDb/doc/hg38/unusualcons.txt new file mode 100644 index 00000000000..a2851d4efb4 --- /dev/null +++ src/hg/makeDb/doc/hg38/unusualcons.txt @@ -0,0 +1,47 @@ +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