9c3a278e681d47532c5e404d43f7019239c60602 kate Mon Oct 14 12:48:13 2019 -0700 Updates to track description, add make doc. refs #23881 diff --git src/hg/makeDb/doc/encode3/mouse.txt src/hg/makeDb/doc/encode3/mouse.txt index ee70c3d..c71b3ea 100644 --- src/hg/makeDb/doc/encode3/mouse.txt +++ src/hg/makeDb/doc/encode3/mouse.txt @@ -1,127 +1,279 @@ ######################### # mm10 histone ChIP-seq from Ren lab # contact: David Gorkin # # (2019-07-03 kate) # # Expecting 3 tracks: # 1. Large composite of ChIP-seq peaks and signal from various marks in various tissues at # different embryonic stages, along with chromHMM for each mark/tissue/stage # (chromHMM may be better as separate track) # # 2. ATAC-seq (open chromatin) for tissues/stages # # 3. Possible: enhancer/gene interactions in interact format # RM #23693 # Their hub: http://renlab.sdsc.edu/yanxiao/encode_trackhub/hub.txt # Download files listed in track hub wget http://renlab.sdsc.edu/yanxiao/encode_trackhub/mm10/trackDb.txt # winnow to just merged files: raToLines trackDb.txt stdout | grep Merge > trackDb.merge.lines wc -l trackDb.merge.lines # 1128 linesToRa trackDb.merge.lines trackDb.merge.ra grep bigDataUrl trackDb.merge.ra | sed -e 's/bigDataUrl/wget/' -e 's/.proxy=true//' > wget.csh mkdir data cd data csh ../wget.csh >&! ../wget.log & ls *.bigBed | wc -l # 563 # These are narrowPeak files, however they are configured in hub as bigBed 6 + # This config shows track colors (e.g. red for repressive, green for promoter), but # doesn't allow filtering on pValue, etc. # Use files as is from portal, we are not changing so no need to rename ln -s `pwd` /gbdb/mm10/encode3/histones ################### # chromHMM data cd .. mkdir chromHmm cd chromHmm wget http://enhancer.sdsc.edu/enhancer_export/ENCODE/chromHMM/readme mkdir pooled cd pooled csh ../wget.csh >&! wget.log & ls *.bb | perl rename.pl > rename.txt cp rename.txt rename.csh # edit rename.csh to symlink files to /gbdb/mm10/encode3/chromHmm ################################################# # ATAC-seq from Ren lab # (kate) # Download signals (.bw) and pooled peaks from Ren lab wget -r -A bw,pooled_peaks.narrowPeak http://renlab.sdsc.edu/yanxiao/encode_trackhub/mm10/atacseq mkdir lab # move files to lab dir # Reuse hub config # http://renlab.sdsc.edu/yanxiao/encode_trackhub/ wget http://renlab.sdsc.edu/yanxiao/encode_trackhub/mm10/trackDb.txt cp /hive/data/outside/encode3/mouse/chromHmm/tracks/rename.pl . # edit for this track. Script will take file list and generate a trackDb and file rename/link script cd lab ls *.bw *.narrowPeak | perl ../rename.pl > ../rename.csh # oops, need to biggify the narrowPeaks (and zero out scores, some of which exceed 1000) set sizes = /hive/data/genomes/mm10/chrom.sizes foreach f (*.narrowPeak) set d = $f:r mv $f $d.narrowPeak.bad awk 'OFS="\t" {$5 = 0; print}' < $d.narrowPeak.bad > $d.narrowPeak bedToBigBed -type=bed6+4 -as=$HOME/kent/src/hg/lib/bigNarrowPeak.as $d.narrowPeak $sizes $d.bb end linesToRa trackDb.atac.lines trackDb.atac.ra cd .. mkdir /gbdb/mm10/encode3/atac csh rename.csh mv trackDb.atac.ra ~/kent/src/hg/makeDb/trackDb/mouse/mm10 # edit for indents, add views ################################################# # Update peak files, from Dave Gorkin at Ren Lab # Overlapping peaks merged, score field set # 09-09-2019 mkdir lab2; cd lab2 wget -A bed -r -nd http://enhancer.sdsc.edu/enhancer_export/ENCODE/for_ucsc/atac_pooled_peaks/ # oops, they have decimal points in score. Strip these. // biggify set sizes = /hive/data/genomes/mm10/chrom.sizes foreach f (*.bed) set d = $f:r sed 's/\..*//' < $d.bed > $d.fixed.bed bedToBigBed -type=bed5 $d.fixed.bed $sizes $d.bb end # link to /gbdb rm /hive/data/gbdb/mm10/encode3/atac/*.bb csh rename2.bb.csh +###################################################################################### +# Interact tracks from Ren Lab enhancer/gene map, with EPDnew promoters (JK rec) + +# (kate July 2019) + +################# +# Download spreadsheet from Dropbox copy provided by Dave Gorkin +# https://www.dropbox.com/s/ksxt9k2dh46k2ya/Gorkin_Ren_tableS5-11.xlsx?dl=0 + +# Gorkin_Ren_EnhancerGene_Rep1.txt + +dos2unix Gorkin_Ren_EnhancerGene_Rep1.txt +tr '\r' '\n' < Gorkin* > enhancerGene.rep1.txt + +# edit out title line +head -1 enhancerGene.rep1.txt +# chrom start end ensembl symbol SCC Z p-value (z) p-value (empirical) +# chr1 4426300 4428300 ENSMUSG00000025902.9 Sox17 6.16E-01 2.07E+00 0.018999025 0.016378526 + +# The SCC field will be basis of score. It ranges from .25 to 1.0 + +# strip trailing empty lines (from bad XLS export) + +################# +# Download promoters from EPDnew (rec from JK) +# https://epd.epfl.ch/EPDnew_database.php + +wget ftp://ccg.epfl.ch/epdnew/README +wget ftp://ccg.epfl.ch/epdnew/M_musculus/003/cross_references.txt . + +# corrupted file ? First line: + +wget ftp://ccg.epfl.ch/epdnew/M_musculus/current/Mm_EPDnew.bed + +# This is version 3, file dated 6/4/18 + +# NOTE: file contains 1 or more promoters per gene. +# Based on conversations with provider (Philip Bucher), we will merge into a single promoter region + +wc -l Mmn_EPDnew.bed +# 25111 + +sed 's/_.*900 / 900 /' MM_EPDnew.bed > promoters.temp.bed +bedtools groupby -g 1,4,5,6 -c 2,3 -o min,max < promoters.temp.bed | \ + awk '{OFS="\t"; print $1, $5, $6, $2, $3, $4}' | \ + bedSort stdin promoters.bed + +wc -l promoters.bed +# 20549 +# Reduced by 5000 + +################# +# Create interact file from interactions and promoters files + +perl makeInteract.pl enhancerGene.rep1.txt MM_EPDnew.bed cross_references.txt >&! errors.txt + +# strip first two lines from enhancerGene file to make map.rep1.txt +#perl makeInteract.pl map.rep1.txt promoters.bed cross_references.txt > enhancerGeneInteract.bed +#Found 30793 interactions with promoters, 1171 with missing promoters + +# NOTE: Missing 374 promoters (will need to get these from GB annotation) + +# NOTE: Problem with cross-references file. At least one instance of error +# Here the ENSG 65324 should be Eno1, not Eno1b (acc to GENCODE V20) +ENSMUSG00000059040 Eno1b NM_001025388 Mus musculus enolase 1B, retrotransposed (Eno1b), mRNA. +ENSMUSG00000063524 Eno1b NM_023119 Mus musculus enolase 1B, retrotransposed (Eno1b), mRNA. + +# NOTE: Problem with duplicated interactions in enhancerGene file -- 2 ENSG's mapped to two +# gene names (so interactions appear twice): + +chr17 13666000 13671200 ENSMUSG00000038347.10 Tcte2 8.69E-01 1.85E+00 0.03221258 0.002229654 +chr17 13666000 13671200 ENSMUSG00000038347.10 2700054A10Rik 8.69E-01 1.85E+00 0.03221258 0.002229654 + +chr12 57514900 57516900 ENSMUSG00000046782.10 4921506M07Rik 4.82E-01 1.75E+00 0.039890209 0.04302926 +chr12 57514900 57516900 ENSMUSG00000046782.10 Ttc6 4.82E-01 1.75E+00 0.039890209 0.04302926 + + +bedSort enhancerGene.rep1.txt.out encode3EnhancerPromoterInteract.bed + +# Biggify interactions +mkdir gbdb +set sizes = /hive/data/genomes/mm10/chrom.sizes +bedToBigBed -type=bed5+13 -as=enhancerPromoterInteract.as encode3EnhancerPromoterInteract.bed \ + $sizes gbdb/encode3EnhancerPromoterInteract.bb +cd /gbdb +ln -s `pwd`/encode3EnhancerPromoterInteract.bb /gbdb/mm10/bbi +cd .. + +# Biggify promoters file +bedSort MM_EPDnew.bed.out epdPromoters3.bed + +# TODO: add more fields ? +bedToBigBed -type=bed9 epdPromoters3.bed \ + $sizes gbdb/epdProomoters3.bb +cd gbdb +ln -s `pwd`/epdPromoters3.bb /gbdb/mm10/bbi +cd .. + + +# old +#hgLoadBed mm10 -noSort -noBin -type=bed5+13 \ + #-sqlTable=/cluster/home/kate/kent/src/hg/lib/interact.sql -renameSqlTable \ + #encode3EnhancerPromoter enhancerGeneInteract.bed + #encode3RenEnhancerGeneInteract enhancerGeneInteract.bed + + +# merge replicates, stripping extra columns, adding a column for count. + +# export from spreadsheet. Trim empty lines. dos2unix. tr \m's to \n's. +wc -l map.* + 31964 map.rep1.txt + 33301 map.rep2.txt + 21142 map.replicated.txt + +perl mergeReps.pl map.rep1.txt map.rep2.txt | bedSort stdin map.merged.txt + +mkdir out +perl makeInteract.pl map.merged.txt MM_EPDnew.bed cross_references.txt out/ >&! makeInteract.log +bedSort out/enhancers.all.bed out/enhancers.all.sorted.bed +bedSort out/enhancers.rep.bed out/enhancers.rep.sorted.bed + +# why needed ??? +bedSort out/interactions.all.bed out/interactions.all.sorted.bed +bedSort out/interactions.rep.bed out/interactions.rep.sorted.bed + +# biggify +set sizes = /hive/data/genomes/mm10/chrom.sizes +bedToBigBed -type=bed5+14 -as=enhancerPromoterInteract.as out/interactions.all.sorted.bed \ + $sizes gbdb/encode3EnhancerPromoterInteractAll.bb +bedToBigBed -type=bed5+14 -as=enhancerPromoterInteract.as out/interactions.rep.sorted.bed \ + $sizes gbdb/encode3EnhancerPromoterInteractRep.bb + +# TODO: add more fields +bedToBigBed -type=bed9 out/promoters.all.bed \ + $sizes gbdb/epdPromoterAll.bb +bedToBigBed -type=bed9 out/promoters.rep.bed \ + $sizes gbdb/epdPromoterRep.bb + +bedToBigBed -type=bed4 out/enhancers.all.sorted.bed \ + $sizes gbdb/encode3EnhancerAll.bb +bedToBigBed -type=bed4 out/enhancers.rep.sorted.bed \ + $sizes gbdb/encode3EnhancerRep.bb +cd gbdb +foreach f (epdPromoterAll epdPromoterRep encode3EnhancerAll encode3EnhancerRep encode3EnhancerPromoterInteractAll encode3EnhancerPromoterInteractRep) + ln -s `pwd`/$f.bb /gbdb/mm10/bbi +end + +cd gbdb +ln -s `pwd`/epdPromoters3.bb /gbdb/mm10/bbi + +# NOTE: Renamed .bb files to prefix w/ encode3Ren/encode3RenInteract +