dfa6639914399df4d023ebc3df4f4009238c645e kate Mon May 4 16:50:39 2020 -0700 Fix chron order in make doc. refs #25130 diff --git src/hg/makeDb/doc/hg38/gtex.txt src/hg/makeDb/doc/hg38/gtex.txt index 16d10b5..5a5303e 100644 --- src/hg/makeDb/doc/hg38/gtex.txt +++ src/hg/makeDb/doc/hg38/gtex.txt @@ -1,145 +1,142 @@ ############################################################################# -# GTEx V8 (Apr 2020) Kate -# Create BED from hgFixed tables (see doc/gtex) - -# Load gene models (Gencode V26 transcript union from GTEx) - -cd /hive/data/outside/gtex/V8/rnaSeq -gtfToGenePred gencode.v26.GRCh38.genes.gtf gencodeV26.hg38.genePred \ - -infoOut=gtexGeneModelInfoV8.tab -hgLoadGenePred hg38 gtexGeneModelV8 gencodeV26.hg38.genePred - -# Get transcript for each gene (why ?) -tail -n +2 gtexGeneModelInfoV8.tab | awk '{printf("%s\t%s\n", $1, $9)}' > gtexGeneTranscriptsV8.tab -#hgLoadSqlTab hgFixed gtexTranscriptV8 ~/kent/src/hg/lib/gtexTranscript.sql gtexGeneTranscriptsV8.tab -# no schema (or table on hgwdev.hgFixed) - -# Load BED table -cd /hive/data/genomes/hg38/bed/gtex -mkdir V8 -cd V8 - -set gencode = V26 -~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed \ - hg38 -noLoad -gtexVersion=V8 -gencodeVersion=$gencode gtexGeneV8 -verbose=2 >&! log.txt & - -Reading wgEncodeGencodeAttrs table -Reading gtexGeneModelV8 table -Reading gtexTissueMedian table -Writing tab file gtexGeneV8 -Max score: 267400.000000 - -# Add scores -set bedScore = ~/kent/src/utils/bedScore/bedScore -$bedScore -col=10 -minScore=0 -log -method=encode gtexGeneV8.tab gtexGeneBedV8.bed -textHistogram -real -autoScale=14 -log -col=5 gtexGeneBedV8.bed -0.000000 ************************************************************ 21287 -71.428643 **************************************************** 5635 -142.857286 **************************************************** 5513 -214.285929 *************************************************** 4683 -285.714571 *************************************************** 4480 -357.143214 *************************************************** 4748 -428.571857 **************************************************** 5466 -500.000500 ************************************************ 3117 -571.429143 ***************************************** 911 -642.857786 ********************************* 252 -714.286429 ************************** 81 -785.715071 ************** 11 -857.143714 ******** 4 -928.572357 *************** 12 - -# load up -set lib = ~/kent/src/hg/lib -hgLoadBed hg38 -noBin -tab -type=bed6+4 \ - -as=$lib/gtexGeneBed.as -sqlTable=$lib/gtexGeneBed.sql -renameSqlTable \ - gtexGeneV8 gtexGeneBedV8.bed -#Read 56200 elements of size 10 from gtexGeneBedV8.bed - - -### TODO -# Add GTEx to Gene Sorter (2016-08-18 kate) -# See hg/near/makeNear.doc - - -############################################################################# # GTEx V6 (October 2015) Kate # Create BED from hgFixed tables (see doc/gtex) # Reloading during QA of track (fixing gene classes, adding scores). (March 2016) Kate cd /hive/data/outside/gtex/V6 # see doc/hg19.txt for how this genePred was made set chain = /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz liftOver -genePred gencodeV19.hg19.genePred $chain gtexGeneModelV6.hg38.genePred \ gencode.V19.hg38.unmapped # 926 unmapped hgLoadGenePred hg38 gtexGeneModelV6 gtexGeneModelV6.hg38.genePred # OLD: creates gtexGeneModelV6.hg38.genePred # OLD: NOTE: drops 192 transcripts. One I spot-checked indeed didn't exist in our hg38 genes cd /hive/data/genomes/hg38/bed mkdir -p gtex cd gtex # table renamed to gtexGeneModel later # Use latest GENCODE attrs file to get biotypes # create bed table ~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed hg38 -gtexVersion=V6 \ -noLoad -gencodeVersion=$gencodeVersion gtexGeneBedV6 -verbose=2 >&! makeGeneBed.log # 45 genes not found in GENCODE attributes table #Max score: 219385.906250 wc -l *.tab wc -l *.tab 52896 gtexGeneBedV6.tab # 55810 gtexGeneBedV6.tab # exploratory for assigning score based on sum of scores (expScores field) set bedScore = ~/kent/src/utils/bedScore/bedScore $bedScore -col=10 -minScore=1 -method=std2 gtexGeneBedV6.tab gtexGeneBedV6.std2.bed $bedScore -col=10 -minScore=1 -method=encode gtexGeneBedV6.tab gtexGeneBedV6.encode.bed $bedScore -col=10 -minScore=1 -method=reg gtexGeneBedV6.tab gtexGeneBedV6.reg.bed $bedScore -col=10 -minScore=1 -method=asinh gtexGeneBedV6.tab gtexGeneBedV6.asinh.bed $bedScore -col=10 -minScore=1 -method=reg -log gtexGeneBedV6.tab gtexGeneBedV6.reg.log.bed $bedScore -log -col=10 -minScore=1 -method=std2 gtexGeneBedV6.tab gtexGeneBedV6.std2.log.bed $bedScore -log -col=10 -minScore=1 -method=encode gtexGeneBedV6.tab gtexGeneBedV6.encode.log.bed $bedScore -log -col=10 -minScore=1 -method=asinh gtexGeneBedV6.tab gtexGeneBedV6.asinh.log.bed # Using -log -method=encode, as this is closest to density plot of all scores # as here: GtexTotalExpressionDensity.png, GtexTotalExpressionFrequency.png textHistogram -real -autoScale=14 -log -col=5 gtexGeneBedV6.encode.log.bed 1.000000 ************************************************************ 22889 72.357214 *************************************************** 4862 143.714428 ************************************************** 4199 215.071643 ************************************************* 3931 286.428857 ************************************************** 4329 357.786071 *************************************************** 5419 429.143285 ************************************************** 4472 500.500500 ********************************************* 1953 571.857714 ************************************** 564 643.214928 ******************************** 200 714.572142 ************************* 61 785.929356 *********** 6 857.286571 ******** 4 928.643785 ************ 7 $bedScore -col=10 -minScore=0 -log -method=encode gtexGeneBedV6.tab gtexGeneBedV6.bed # load up set lib = ~/kent/src/hg/lib hgLoadBed hg38 -noBin -tab -type=bed6+4 \ -as=$lib/gtexGeneBed.as -sqlTable=$lib/gtexGeneBed.sql -renameSqlTable \ gtexGeneBedNewV6 gtexGeneBedV6.bed # Add GTEx to Gene Sorter (2016-08-18 kate) # See hg/near/makeNear.doc +############################################################################# +# GTEx V8 (Apr 2020) Kate +# Create BED from hgFixed tables (see doc/gtex) + +# Load gene models (Gencode V26 transcript union from GTEx) + +cd /hive/data/outside/gtex/V8/rnaSeq +gtfToGenePred gencode.v26.GRCh38.genes.gtf gencodeV26.hg38.genePred \ + -infoOut=gtexGeneModelInfoV8.tab +hgLoadGenePred hg38 gtexGeneModelV8 gencodeV26.hg38.genePred + +# Get transcript for each gene (why ?) +tail -n +2 gtexGeneModelInfoV8.tab | awk '{printf("%s\t%s\n", $1, $9)}' > gtexGeneTranscriptsV8.tab +#hgLoadSqlTab hgFixed gtexTranscriptV8 ~/kent/src/hg/lib/gtexTranscript.sql gtexGeneTranscriptsV8.tab +# no schema (or table on hgwdev.hgFixed) + +# Load BED table +cd /hive/data/genomes/hg38/bed/gtex +mkdir V8 +cd V8 + +set gencode = V26 +~/kent/src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed \ + hg38 -noLoad -gtexVersion=V8 -gencodeVersion=$gencode gtexGeneV8 -verbose=2 >&! log.txt & + +Reading wgEncodeGencodeAttrs table +Reading gtexGeneModelV8 table +Reading gtexTissueMedian table +Writing tab file gtexGeneV8 +Max score: 267400.000000 +# Add scores +set bedScore = ~/kent/src/utils/bedScore/bedScore +$bedScore -col=10 -minScore=0 -log -method=encode gtexGeneV8.tab gtexGeneBedV8.bed +textHistogram -real -autoScale=14 -log -col=5 gtexGeneBedV8.bed +0.000000 ************************************************************ 21287 +71.428643 **************************************************** 5635 +142.857286 **************************************************** 5513 +214.285929 *************************************************** 4683 +285.714571 *************************************************** 4480 +357.143214 *************************************************** 4748 +428.571857 **************************************************** 5466 +500.000500 ************************************************ 3117 +571.429143 ***************************************** 911 +642.857786 ********************************* 252 +714.286429 ************************** 81 +785.715071 ************** 11 +857.143714 ******** 4 +928.572357 *************** 12 + +# load up +set lib = ~/kent/src/hg/lib +hgLoadBed hg38 -noBin -tab -type=bed6+4 \ + -as=$lib/gtexGeneBed.as -sqlTable=$lib/gtexGeneBed.sql -renameSqlTable \ + gtexGeneV8 gtexGeneBedV8.bed +#Read 56200 elements of size 10 from gtexGeneBedV8.bed + + +### TODO +# Add GTEx to Gene Sorter (2016-08-18 kate) +# See hg/near/makeNear.doc