be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/doc/hg38/ncbiRefSeq.txt src/hg/makeDb/doc/hg38/ncbiRefSeq.txt index b443fcb..d65f817 100644 --- src/hg/makeDb/doc/hg38/ncbiRefSeq.txt +++ src/hg/makeDb/doc/hg38/ncbiRefSeq.txt @@ -1,339 +1,340 @@ # for emacs: -*- mode: sh; -*- # This file describes the construction of NCBI RefSeq track -- latest first ######################################################################### # ncbiRefSeq.p11 Genes (DONE - 2018-01-09 - Angie) # Previously done 2017-09-28; redone 11-16 to include mito "rna" from chrM genomic seq; # redone 2018-01-09 to pick up changes in NCBI download files from 2017-12-22 mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq.p11.2018-01-09 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p11.2018-01-09 time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.37_GRCh38.p11 hg38) > do.log 2>&1 & tail -f do.log # *** All done ! Elapsed time: 23m51s # real 23m51.091s cat fb.ncbiRefSeq.hg38.txt # 129593530 bases of 3049335806 (4.250%) in intersection ######################################################################### ######################################################################### # ncbiRefSeq.p8 Genes (DONE - 2016-08-18 - Hiram) mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq.p8 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p8 # running step wise as this script is still under development time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.34_GRCh38.p8 hg38) > download.log 2>&1 # real 12m35.601s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.34_GRCh38.p8 hg38) > process.log 2>&1 # real 14m18.953s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=load -bigClusterHub=ku -dbHost=hgwdev \ -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.34_GRCh38.p8 hg38) > load.log 2>&1 # real 0m59.189s cat fb.ncbiRefSeq.hg38.txt # 141131948 bases of 3049335806 (4.628%) in intersection ############################################################################# ######################################################################### # ncbiRefSeq.p7 Genes (DONE - 2016-05-20 - Hiram) mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq.p7 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p7 # running step wise as this script is still under development time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.33_GRCh38.p7 hg38) > download.log 2>&1 # real 12m35.601s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.33_GRCh38.p7 hg38) > process.log 2>&1 # real 14m18.953s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=load -bigClusterHub=ku -dbHost=hgwdev \ -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.33_GRCh38.p7 hg38) > load.log 2>&1 # real 0m59.189s cat fb.ncbiRefSeq.hg38.txt # 141131948 bases of 3049335806 (4.628%) in intersection ############################################################################# mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq cd /hive/data/genomes/hg38/bed/ncbiRefSeq export asmName="GCF_000001405.31_GRCh38.p5" # most of these files could be linked in from the refseq download, for example: ln -s /hive/data/genomes/hg38/refseq/${asmName}_rna.gbff.gz ./ # or, fetched freshly from NCBI refseq assemblies: for F in ${asmName}_genomic.fna.gz ${asmName}_genomic.gff.gz \ ${asmName}_rna.fna.gz ${asmName}_assembly_report.txt do time rsync -L -a -P rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/latest_assembly_versions/${asmName}/${F} ./ done # measure these items: faCount ${asmName}_rna.fna.gz > rna.faCount.txt faCount ${asmName}_genomic.fna.gz > genomic.faCount.txt egrep -v "^#seq|^total" rna.faCount.txt | cut -f1,2 \ | sort -k2nr > rna.chrom.sizes egrep -v "^#seq|^total" genomic.faCount.txt | cut -f1,2 \ | sort -k2nr > genomic.chrom.sizes # this constructes the unlifted genePred file with NCBI chrom names gff3ToGenePred -useName -attrsOut=${asmName}.attrs.useName.txt \ ${asmName}_genomic.gff.gz \ ${asmName}.useName.gp # extract additional names from column nine to use as an index for # the variety of names that identify each item ~/kent/src/hg/makeDb/doc/hg38/gffToIx.pl ${asmName}_genomic.gff.gz \ > ${asmName}_genomic.ix.txt # for psl alignments, only need to work on the items with Gap specifications # The NG_ named items do not function correctly zgrep -v "NG_" ${asmName}_genomic.gff.gz | grep "Gap=" >> only.gap.gff # construct the PSL alignments from the Gap records sed -e 's/cDNA_match/match/;' only.gap.gff \ | gff3ToPsl genomic.chrom.sizes rna.chrom.sizes stdin ${asmName}.psl # this doesn't work, too many UCSC names missing from the NCBI file: grep -v "^#" ${asmName}_assembly_report.txt | sed -e 's/^M//g;' \ | cut -f7,9,10 \ |awk -F'\t' '{printf "0\t%s\t%d\t%s\t%d\n", $1, $2, $3, $2}' \ > insdcToHg38.lift # the automated hubs process does construct a good NCBI to UCSC lift file: export liftFile="/hive/data/inside/ncbi/genomes/refseq/vertebrate_mammalian/Homo_sapiens/latest_assembly_versions/${asmName}/${asmName}.ncbiToUcsc.lift" # liftUp the genePred from NCBI chrom names to UCSC chrom names liftUp -extGenePred -type=.gp stdout \ ${liftFile} warn ${asmName}.useName.gp | gzip -c \ > ${asmName}.ucsc.gp.gz touch -r ${asmName}.useName.gp ${asmName}.ucsc.gp.gz # some items will fail because they are on patches or alternative sequence # from Patch 5 that does not exist in hg38 genePredCheck -db=hg38 ${asmName}.ucsc.gp.gz # checked: 150709 failed: 1455 # filter out the patches and alternative sequences that are not in hg38 genePredFilter -db=hg38 ${asmName}.ucsc.gp.gz stdout \ | gzip -c > ${asmName}.hg38.gp.gz # this should be perfectly good genePredCheck -db=hg38 ${asmName}.hg38.gp.gz # checked: 149254 failed: 0 # liftUp the psl file from NCBI chrom names to UCSC chrom names pslSwap ${asmName}.psl stdout \ | liftUp -type=.psl stdout ${liftFile} drop stdin \ | gzip -c > ${asmName}.ucsc.psl.gz touch -r ${asmName}.psl ${asmName}.ucsc.psl.gz # same problem here as above, not everything is in hg38, # filter patch 5 items out: pslCheck -pass=stdout -db=hg38 ${asmName}.ucsc.psl.gz 2> /dev/null \ | gzip -c > ${asmName}.hg38.psl.gz pslCheck -db=hg38 ${asmName}.hg38.psl.gz # checked: 1062 failed: 0 errors: 0 # separate categories of genes: zegrep "^N(M|R)|^YP" ${asmName}.hg38.gp.gz > curated.gp zegrep "^X(M|R)" ${asmName}.hg38.gp.gz > predicted.gp zegrep -v "^N(M|R)|^YP|X(M|R)" ${asmName}.hg38.gp.gz > other.gp # verify none lost wc -l curated.gp predicted.gp other.gp 54869 curated.gp 88703 predicted.gp 5682 other.gp 149254 total zcat ${asmName}.hg38.gp.gz | wc -l 149254 # extract CDS records from the rna.gbff.gz for bigPsl construction: ~/kent/src/hg/makeDb/doc/hg38/gbffToCds.pl ${asmName}_rna.gbff.gz > rna.cds # ensure simple names are in the rna.fa file zcat ${asmName}_rna.fna.gz | sed -e 's/ .*//;' > rna.fa pslToBigPsl -fa=rna.fa -cds=rna.cds ${asmName}.hg38.psl.gz test.bigPsl sort -k1,1 -k2,2n test.bigPsl > ${asmName}.hg38.bigPsl bedToBigBed -type=bed12+12 -tab -as=$HOME/kent/src/hg/lib/bigPsl.as \ ${asmName}.hg38.bigPsl ../../chrom.sizes ${asmName}.hg38.bigPsl.bb # loading genePred tracks: hgLoadGenePred -genePredExt hg38 ncbiRefSeqCurated curated.gp genePredCheck -db=hg38 ncbiRefSeqCurated # checked: 54869 failed: 0 hgLoadGenePred -genePredExt hg38 ncbiRefSeqPredicted predicted.gp genePredCheck -db=hg38 ncbiRefSeqPredicted # checked: 88703 failed: 0 hgLoadGenePred -genePredExt hg38 ncbiRefSeqOther other.gp genePredCheck -db=hg38 ncbiRefSeqOther # checked: 5682 failed: 0 ########## early experiment, not used later # # and the bigPsl file: # mkdir -p /gbdb/hg38/bbi/ncbiRefSeq # ln -s `pwd`/${asmName}.hg38.bigPsl.bb /gbdb/hg38/bbi/ncbiRefSeqBigPsl.bb # hgBbiDbLink hg38 ncbiRefSeqBigPsl /gbdb/hg38/bbi/ncbiRefSeqBigPsl.bb ########## early experiment, not used later ############################################################################# # addition of HGMD-restricted subset, Max, Jan 29 2019 # updated Dec 2019 -cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2019-12-06/ +# updated Dec 2020 +cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2020-10-27/ # change in 2019: ignore the version numbers, otherwise only 1815 transcripts left, big update by HGMD in 2019? # adding "." so NM_123 doesn't match NM_123123 cat /hive/data/outside/hgmd/$year.4-hgmd-public_hg38.tsv | cut -f7 | cut -d. -f1 | sort -u | awk '{print $1"."}' > hgmdTranscripts.txt zcat process/hg38.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp hgLoadGenePred -genePredExt hg38 ncbiRefSeqHgmd hgmd.curated.gp ############################################################################# # ncbiRefSeq.p13 update (DONE - 2019-12-06 - Hiram) # current version information cat /gbdb/hg38/ncbiRefSeq/ncbiRefSeqVersion.txt # NCBI Homo sapiens Annotation Release 109 (2018-03-29) # Version information from the file: # /hive/data/outside/ncbi/genomes/refseq/vertebrate_mammalian/Homo_sapiens/ # all_assembly_versions/GCF_000001405.39_GRCh38.p13/ # GCF_000001405.39_GRCh38.p13_genomic.gff.gz #!annotation-date 09/05/2019 #!annotation-source NCBI Homo sapiens Updated Annotation Release 109.20190905 mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2019-12-06 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2019-12-06 ### BEFORE loading this updated table featureBits -countGaps hg38 ncbiRefSeq # 134109466 bases of 3257347282 (4.117%) in intersection featureBits -enrichment hg38 refGene ncbiRefSeq # refGene 3.098%, ncbiRefSeq 4.332%, both 2.920%, cover 94.23%, enrich 21.75x featureBits -enrichment hg38 ncbiRefSeq refGene # ncbiRefSeq 4.332%, refGene 3.098%, both 2.920%, cover 67.40%, enrich 21.75x featureBits -enrichment hg38 ncbiRefSeqCurated refGene # ncbiRefSeqCurated 2.880%, refGene 3.098%, both 2.846%, cover 98.84%, enrich 31.90x featureBits -enrichment hg38 refGene ncbiRefSeqCurated # refGene 3.098%, ncbiRefSeqCurated 2.880%, both 2.846%, cover 91.86%, enrich 31.90x # running step wise just to be careful time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.39_GRCh38.p13 hg38) > download.log 2>&1 # real 3m23.090s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=process -bigClusterHub=ku -dbHost=hgwdev \ -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.39_GRCh38.p13 hg38) > process.log 2>&1 # real 6m10.922s time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -continue=load -bigClusterHub=ku -dbHost=hgwdev \ -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \ refseq vertebrate_mammalian Homo_sapiens \ GCF_000001405.39_GRCh38.p13 hg38) > load.log 2>&1 # real 0m41.366s ### AFTER loading this updated table # compare this result: cat fb.ncbiRefSeq.hg38.txt # 136778258 bases of 3095998939 (4.418%) in intersection # with previous version existing table (from fb above): # 134109466 bases of 3257347282 (4.117%) in intersection featureBits -enrichment hg38 refGene ncbiRefSeq # refGene 3.098%, ncbiRefSeq 4.418%, both 3.073%, cover 99.19%, enrich 22.45x # previous: # refGene 3.098%, ncbiRefSeq 4.332%, both 2.920%, cover 94.23%, enrich 21.75x featureBits -enrichment hg38 ncbiRefSeq refGene # ncbiRefSeq 4.418%, refGene 3.098%, both 3.073%, cover 69.56%, enrich 22.45x # previous: # ncbiRefSeq 4.332%, refGene 3.098%, both 2.920%, cover 67.40%, enrich 21.75x featureBits -enrichment hg38 ncbiRefSeqCurated refGene # ncbiRefSeqCurated 3.073%, refGene 3.098%, both 3.067%, cover 99.81%, enrich 32.22x # previous: # ncbiRefSeqCurated 2.880%, refGene 3.098%, both 2.846%, cover 98.84%, enrich 31.90x featureBits -enrichment hg38 refGene ncbiRefSeqCurated # refGene 3.098%, ncbiRefSeqCurated 3.073%, both 3.067%, cover 98.99%, enrich 32.22x # previous: # refGene 3.098%, ncbiRefSeqCurated 2.880%, both 2.846%, cover 91.86%, enrich 31.90x ######################################################################### # addition of RefSeq Select-restricted subset, Max, Feb 10 2019 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2019-12-06/ zcat download/*_genomic.gff.gz | egrep 'tag=(RefSeq|MANE) Select' | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt cat process/hg38.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp hgLoadGenePred -genePredExt hg38 ncbiRefSeqSelect refseqSelect.curated.gp wc -l refseqSelect.curated.gp 21071 refseqSelect.curated.gp ############################################################################# ############################################################################# # update 2020-10-27 (DONE - Hiram - 2020-10-27) mkdir /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2020-10-27 cd /hive/data/genomes/hg38/bed/ncbiRefSeq.p13.2020-10-27 time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \ -bigClusterHub=ku -dbHost=hgwdev \ -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \ GCF_000001405.39_GRCh38.p13 hg38) > do.log 2>&1 & # real 11m46.506s cat fb.ncbiRefSeq.hg38.txt # 137385668 bases of 3110768607 (4.416%) in intersection #############################################################################