77ceb7f28c14b899e105395b479a29de88c1e419
galt
  Mon Apr 19 17:47:52 2021 -0700
typographical error hg19 analysisSet

diff --git src/hg/makeDb/doc/hg19.analysisSet.txt src/hg/makeDb/doc/hg19.analysisSet.txt
index aae6fe8..77e8c1b 100644
--- src/hg/makeDb/doc/hg19.analysisSet.txt
+++ src/hg/makeDb/doc/hg19.analysisSet.txt
@@ -1,53 +1,53 @@
 # get NCBI's analysis set fasta files
 mkdir /hive/data/genomes/hg19/bed/analysisSet
 cd /hive/data/genomes/hg19/bed/analysisSet
 wget https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/seqs_for_alignment_pipelines/GCA_000001405.14_GRCh37.p13_full_analysis_set.fna.gz 
 wget https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/seqs_for_alignment_pipelines/GCA_000001405.14_GRCh37.p13_no_alt_analysis_set.fna.gz 
 
 # 298 unique sequence lengths so can use them to join with UCSC sequences
 cat /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/p13.plusMT/hg19.p13.plusMT.chrom.sizes | grep -v 'chrM'$'\t' | sort -k2n > ucscSizes.txt
 faSize GCA_000001405.14_GRCh37.p13_full_analysis_set.fna.gz -detailed | sort -k2n | grep -v chrEBV > ncbiSizes.txt
 # make sure that they match
 paste ncbiSizes.txt ucscSizes.txt  |awk '($1!=$3)' | awk '($2!=$4)'
 # create sed replacement file
 paste ncbiSizes.txt ucscSizes.txt  | awk '($1!=$3) {OFS="\t"; print($1,$3);} ' > ncbiToUcsc.txt
 cat ncbiToUcsc.txt  | awk '{print ("s/"$1"/"$2"/g")}' > ncbiToUcsc.sed
 
 # convert NCBI chroms
 zcat GCA_000001405.14_GRCh37.p13_full_analysis_set.fna.gz | sed -f ncbiToUcsc.sed > hg19.p13.plusMT.full_analysis_set.fa
 zcat GCA_000001405.14_GRCh37.p13_no_alt_analysis_set.fna.gz | sed -f ncbiToUcsc.sed > hg19.p13.plusMT.no_alt_analysis_set.fa &
 gzip hg19.p13.plusMT.no_alt_analysis_set.fa 
 gzip hg19.p13.plusMT.full_analysis_set.fa 
 
 # not sure if anyone needs a 2bit file for these?
 faToTwoBit hg19.p13.plusMT.no_alt_analysis_set.fa.gz hg19.p13.plusMT.no_alt_analysis_set.2bit 
 faToTwoBit hg19.p13.plusMT.full_analysis_set.fa.gz hg19.p13.plusMT.full_analysis_set.2bit
 
 # make table for g1k genome
 twoBitInfo hg19.p13.plusMT.no_alt_analysis_set.2bit stdout | grep -v 'chrEBV' | grep -v 'chrM'$'\t' | sort -k2n > ucscSizes.noAlt.txt
 wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz 
 faSize -detailed human_g1k_v37.fasta.gz > g1k.sizes
 paste g1k.sizes ucscSizes.noAlt.txt |cut -f1,3 > g1kToUcsc.txt
 
 # make table for Ensembl genome
 wget http://ftp.ensembl.org/pub/grch37/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa.gz 
 faSize -detailed Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa.gz > ensemblSizes.txt &
 paste ensemblSizes.txt ucscSizes.noAlt.txt  | cut -f1,3 > ensemblToUcsc.txt
 
 # index for aligners
 mkdir hg19
 zcat hg19.p13.plusMT.no_alt_analysis_set.fa.gz > hg19/hg19.p13.plusMT.no_alt_analysis_set.fa
 cd hg19
 bwa index hg19.p13.plusMT.no_alt_analysis_set.fa
 bowtie2-build hg19.p13.plusMT.no_alt_analysis_set.fa hg19.p13.plusMT.no_alt_analysis_set
 hisat2-build hg19.p13.plusMT.no_alt_analysis_set.fa hg19.p13.plusMT.no_alt_analysis_set
 cd ..
 
 tar cvzf hg19.p13.plusMT.no_alt_analysis_set.bwa_index.tar.gz hg19/*.{pac,amb,ann,bwt,sa}
 tar cvzf hg19.p13.plusMT.no_alt_analysis_set.bowtie2_index.tar.gz hg19/*.bt2
 tar cvzf hg19.p13.plusMT.no_alt_analysis_set.hisat2_index.tar.gz hg19/*.ht2
 
 # copy stuff to webserver
 mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/chromAlias -p
 mv *.2bit hg19.*.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/
-mv *toUcsc.txt /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/chromAlias/
+mv *ToUcsc.txt /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/chromAlias/