6da2767e61846dd7fd6873f9897b72c56622dcda markd Sat May 21 20:48:28 2022 -0700 rename rmsk PNG files diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt index d9d8a81..00aff7a 100644 --- src/hg/makeDb/doc/chm13v2.0userData/build.txt +++ src/hg/makeDb/doc/chm13v2.0userData/build.txt @@ -1,437 +1,437 @@ ================================================================ Notes: dataDir = /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0 stagingDir = /hive/data/genomes/asmHubs/GCA/009/914/755/GCA_009914755.4 T2T CHM13 track spreadsheet https://docs.google.com/spreadsheets/d/13BXuEFB904aje6zWXyZ0znZnXvQiu1qxKADA2uV2JU4/edit#gid=1966247802 staging URL https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt - https://hgwdev.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt&genome=hub_24696_GCA_009914755.4 + https://hgwdev.gi.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt&genome=GCA_009914755.4 https://hgwdev.gi.ucsc.edu/h/GCA_009914755.4 [doesn't work] Public link: https://genome.ucsc.edu/h/GCA_009914755.4 https://hgdownload-test.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt # tmp kentDir=${HOME}/compbio/t2t/projs/chm13-v2.0/kent ================================================================ ucscChromNames (2022-02-22 markd) ---------------------------------------------------------------- Chromosome sizes files with UCSC names for building other tracks, not a track in the browser t2t-chm13-v2.0.2bit t2t-chm13-v2.0.fa.gz t2t-chm13-v2.0.sizes t2t-chm13-v2.0.sizes3 ================================================================ proseq (2022-02-21 markd) ---------------------------------------------------------------- Supplied by Savannah Hoyt <savannah.klein@uconn.edu> from T2T Globus /team-epigenetics/PROseq-RNAseq_chm13v1.1/MappedToCHM13v1.1/PROseq_Bowtie2/ trackData/proseq renaming files to something not as long CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-chm13v1.1_neg.bigwig -> PROseq_default_neg.bw CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-chm13v1.1_pos.bigwig -> PROseq_default_pos.bw CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_meryl-21mer-chm13v1.1_neg.bigwig -> PROseq_k100_21mer_neg.bw CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_meryl-21mer-chm13v1.1_pos.bigwig -> PROseq_k100_21mer_pos.bw CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_neg.bigwig -> PROseq_k100_neg.bw CHM13-AB_proseq_cutadapt-q20-m20_bt2-vs-dM_bt2-k100-chm13v1.1_pos.bigwig -> PROseq_k100_pos.bw PROseq_k100_AB.markersandlength_meryl-21mer-chm13v1.1_neg.bigwig -> PROseq_k100_dual_21mer_neg.bw PROseq_k100_AB.markersandlength_meryl-21mer-chm13v1.1_pos.bigwig -> PROseq_k100_dual_21mer_pos.bw ================================================================ rnaseq (2022-03-02 markd) ---------------------------------------------------------------- Supplied by Savannah Hoyt <savannah.klein@uconn.edu> /team-epigenetics/PROseq-RNAseq_chm13v1.1/MappedToCHM13v1.1/RNAseq_Bowtie2/ renaming files to something not as long CHM13_S182-183_rnaseq_cutadapt-q20-m100_bt2-chm13v1.1_F1548.bigwig -> RNAseq_default.bw CHM13_S182-183_rnaseq_cutadapt-q20-m100_bt2-k100-chm13v1.1_F1548.bigwig -> RNAseq_k100.bw CHM13_S182-S183_rnaseq_cutadapt-q20-m100_bt2-k100-chm13v1.1-F1548_meryl-21mer-chm13v1.1.bigwig -> RNAseq_k100_21mer.bw RNAseq_k100_AB.markersandlength_meryl-21mer-chm13v1.1.bigwig -> RNAseq_k100_dual_21mer.bw ================================================================ cytoBandsMapped (2022-02-22 markd) ---------------------------------------------------------------- cytoBand tracks from T2T project mapped from GRCh38 Supplied by Nick Altemose <nickaltemose@gmail.com> Delivered via Slack trackData/cytoBandMapped bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/cytoBand.as chm13v2.0_cytobands_allchrs.bed../chromAlias/ucsc.sizes.txt cytoBandMapped.bb ================================================================ sedefSegDups (2022-02-24 markd) ---------------------------------------------------------------- Supplied by Mitchell Robert Vollger <mvollger@uw.edu> team-segdups/Assembly_analysis/SEDEF/T2T-CHM13v2.SDs.bed bedToBigBed -as=${kentDir}/src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/schema/sedefSegDups.as -type=bed9+ T2T-CHM13v2.SDs.bed../chromAlias/ucsc.sizes.txt sedefSegDups.bb ================================================================ rdnaModel (2022-03-02 markd) ---------------------------------------------------------------- from Adam Phillippy https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v1.1.rdna_model.bed bedToBigBed -type=bed4 chm13v1.1.rdna_model.bed../chromAlias/ucsc.sizes.txt rdnaModel.bb ================================================================ catLiftOffGenesV1 (2022-03-15 markd) ---------------------------------------------------------------- from Marina Haukness <mhauknes@ucsc.edu> http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.bb http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3 rename to catLiftOffGenesV1.bb catLiftOffGenesV1.gff3.gz # create GTF zcat catLiftOffGenesV1.gff3.gz | gffread /dev/stdin -T -o catLiftOffGenesV1.gtf pigz catLiftOffGenesV1.gtf # obtain sequence fastas http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.fasta http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.protein.fasta mv CHM13.v2.0.fasta catLiftOffGenesV1.rna.fa mv CHM13.v2.0.protein.fasta catLiftOffGenesV1.protein.fa pigz *.fa ================================================================ * hgLiftOver (2022-03-26 markd) ---------------------------------------------------------------- GRCh38 & GRCh37 Nae-Chyun Chen <naechyun.chen@gmail.com> # 2022-04-09 it was noted that chrM was left out of above alignments, so obtain them and repeat # 2022-04-19 it was discover that chains render oddly due to the lack of chain ids. Use chainMergeSort # to fix this globus: /team-liftover/v1_nflo/with_chrM/ chm13v2-grch38.chain grch38-chm13v2.chain chm13v2-hg19_chrM.chain chm13v2-hg19_chrMT.chain hg19_chrM-chm13v2.chain hg19_chrMT-chm13v2.chain cd trackData/hgLiftOver # rename to match UCSC conventions mv chm13v2-grch38.chain chm13v2-hg38.over.no-id.chain mv grch38-chm13v2.chain hg38-chm13v2.over.no-id.chain mv chm13v2-hg19_chrM.chain chm13v2-hg19_chrM.over.no-id.chain mv chm13v2-hg19_chrMT.chain chm13v2-hg19_chrMT.over.no-id.chain mv hg19_chrM-chm13v2.chain hg19_chrM-chm13v2.over.no-id.chain mv hg19_chrMT-chm13v2.chain hg19_chrMT-chm13v2.over.no-id.chain # add chain ids and score chainMergeSort chm13v2-hg19_chrM.over.no-id.chain | chainScore stdin ../ucscChromNames/t2t-chm13-v2.0.2bit /hive/data/genomes/hg19/hg19.2bit chm13v2-hg19_chrM.over.chain & chainMergeSort chm13v2-hg19_chrMT.over.no-id.chain | chainScore stdin ../ucscChromNames/t2t-chm13-v2.0.2bit /hive/data/genomes/hg19/hg19.2bit chm13v2-hg19_chrMT.over.chain & chainMergeSort chm13v2-hg38.over.no-id.chain | chainScore stdin ../ucscChromNames/t2t-chm13-v2.0.2bit /hive/data/genomes/hg38/hg38.2bit chm13v2-hg38.over.chain & chainMergeSort hg19_chrM-chm13v2.over.no-id.chain | chainScore stdin /hive/data/genomes/hg19/hg19.2bit ../ucscChromNames/t2t-chm13-v2.0.2bit hg19_chrM-chm13v2.over.chain & chainMergeSort hg19_chrMT-chm13v2.over.no-id.chain | chainScore stdin /hive/data/genomes/hg19/hg19.2bit ../ucscChromNames/t2t-chm13-v2.0.2bit hg19_chrMT-chm13v2.over.chain & chainMergeSort hg38-chm13v2.over.no-id.chain | chainScore stdin /hive/data/genomes/hg38/hg38.2bit ../ucscChromNames/t2t-chm13-v2.0.2bit hg38-chm13v2.over.chain & # create hg19 chains that combine chrM and chrMT for use in browser. chainFilter -q=chrMT chm13v2-hg19_chrMT.over.chain | chainMergeSort stdin chm13v2-hg19_chrM.over.chain > chm13v2-hg19.over.chain chainFilter -t=chrMT hg19_chrMT-chm13v2.over.chain | chainMergeSort stdin hg19_chrM-chm13v2.over.chain > hg19-chm13v2.over.chain pigz *.chain # build tracks hgLoadChain -noBin -test none bigChain chm13v2-hg38.over.chain.gz sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../chromAlias/ucsc.sizes.txt chm13v2-hg38.over.chain.bb tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab ../chromAlias/ucsc.sizes.txt chm13v2-hg38.over.link.bb hgLoadChain -noBin -test none bigChain chm13v2-hg19.over.chain.gz sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../chromAlias/ucsc.sizes.txt chm13v2-hg19.over.chain.bb tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab ../chromAlias/ucsc.sizes.txt chm13v2-hg19.over.link.bb rm *.tab # make available is liftOver directory as we ln -f *.over.chain.gz ../../liftOver/ # GRCh38 mask used in liftover. This is based on: # https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_GRC_exclusions_T2Tv2.bed # plus UCSC hg38 centromeres track GRCh38: /team-liftover/grch38_masked_fasta/grch38-centromere_and_falsedup.bed (edited) rename to hg38.liftover-mask.bed ln -f hg38.liftover-mask.bed ../../liftOver/ ================================================================ * hgCactus (2022-03-28 markd) ---------------------------------------------------------------- # HAL from Marina Haukness <mhauknes@ucsc.edu> http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/t2tChm13.v2.0.hal # rename genomes to match browser, in renameFile.tab put GRCh38 hg38 CHM13 GCA_009914755.4 halRenameGenomes t2tChm13.v2.0.hal renameFile.tab # NOTE: disabled due to Snakes not using chromAlias ================================================================ * hgUnique (2022-03-30 markd) ---------------------------------------------------------------- regions not in hg38: original version in: globus: /team-liftover/v1_nflo/T2T-CHM13v2.0_new_and_non_syntenic_regions.bed chm13v2-unique_to_hg19.bed chm13v2-unique_to_hg38.bed however, with the addition of # chainToPslBasic ../hgLiftOver/chm13v2-hg38.over.chain.gz stdout \ | pslToBed stdin stdout \ | bedtools sort -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \ | bedtools merge \ | bedtools complement -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \ | bedtools merge \ | sort -k1,1 -k2,2n \ > chm13v2-unique_to_hg38.bed chainToPslBasic ../hgLiftOver/chm13v2-hg19.over.chain.gz stdout \ | pslToBed stdin stdout \ | bedtools sort -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \ | bedtools merge \ | bedtools complement -i - -g ../ucscChromNames/t2t-chm13-v2.0.sizes \ | bedtools merge \ | sort -k1,1 -k2,2n \ > chm13v2-unique_to_hg19.bed bedToBigBed -type=bed3 -tab chm13v2-unique_to_hg38.bed ../chromAlias/ucsc.sizes.txt hgUnique.hg38.bb bedToBigBed -type=bed3 -tab chm13v2-unique_to_hg19.bed ../chromAlias/ucsc.sizes.txt hgUnique.hg19.bb ================================================================ * censat (2022-03-29 markd) ---------------------------------------------------------------- from Nick Altemose <nickaltemose@gmail.com> via Slack: t2t_censat_CHM13v2.0_trackv2.0.10col.bed t2t_censat_CHM13v2.0_trackv2.0_description.html cd censat/ # drop track header tawk 'NR>1' t2t_censat_CHM13v2.0_trackv2.0.10col.bed | csort -k1,1 -k2,2n >tmp.bed bedToBigBed -type=bed9+1 -as=${HOME}/compbio/t2t/projs/chm13-v2.0/makeDir/schema/cenSat.as -tab tmp.bed ../chromAlias/ucsc.sizes.txt censat.bb ================================================================ * dbSNP155 (2022-03-29 markd) ---------------------------------------------------------------- # dbSNP Variants Lifted+Recovered Dylan Taylor https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/liftover/chm13v2.0_dbSNPv155.vcf.gz dbSNP_lifted-recovered.html # need to use NCBI names until supported by chromAlias zcat chm13v2.0_dbSNPv155.vcf.gz | chromToUcsc --chromAlias=../chromAlias/GCA_009914755.4_T2T-CHM13v2.0.chromAlias.txt /dev/stdin | bgzip -c >chm13v2.0_dbSNPv155.ncbi-names.vcf.gz tabix -p vcf chm13v2.0_dbSNPv155.vcf.gz & tabix -p vcf chm13v2.0_dbSNPv155.ncbi-names.vcf.gz & ================================================================ * clinVar20220313 (2022-03-29 markd) ---------------------------------------------------------------- ClinVar Lifted+Recovered Dylan Taylor https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/liftover/chm13v2.0_ClinVar20220313.vcf.gz zcat chm13v2.0_ClinVar20220313.vcf.gz | chromToUcsc --chromAlias=../chromAlias/GCA_009914755.4_T2T-CHM13v2.0.chromAlias.txt /dev/stdin | bgzip -c >chm13v2.0_ClinVar20220313.ncbi-names.vcf.gz tabix -p vcf chm13v2.0_ClinVar20220313.vcf.gz & tabix -p vcf chm13v2.0_ClinVar20220313.ncbi-names.vcf.gz & ================================================================ * gwasSNPs2022-03-08 (2022-03-29 markd) ---------------------------------------------------------------- GWAS SNPs Lifted+Recovered TBD Dylan Taylor https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/liftover/chm13v2.0_GWASv1.0rsids_e100_r2022-03-08.vcf.gz gwas_catalog_lifted-recovered.html # need to use NCBI names until supported by chromAlias zcat chm13v2.0_GWASv1.0rsids_e100_r2022-03-08.vcf.gz | chromToUcsc --chromAlias=../chromAlias/GCA_009914755.4_T2T-CHM13v2.0.chromAlias.txt /dev/stdin | bgzip -c >chm13v2.0_GWASv1.0rsids_e100_r2022-03-08.ncbi-names.vcf.gz tabix -p vcf chm13v2.0_GWASv1.0rsids_e100_r2022-03-08.ncbi-names.vcf.gz& tabix -p vcf chm13v2.0_GWASv1.0rsids_e100_r2022-03-08.vcf.gz& ================================================================ * microsatellites (2022-04-17 markd) ---------------------------------------------------------------- Arang Rhie doc https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/microsatellite.html GA https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.GA.128.wig TC https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.TC.128.wig GC https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.GC.128.wig AT https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.AT.128.wig # convert to bigWi for f in *.wig ; do wigToBigWig -clip $f ../ucscChromNames/t2t-chm13-v2.0.sizes $(basename $f .wig).bw ; done pigz *.wig ================================================================ * sgdpCopyNumber (2022-04-25 markd) ---------------------------------------------------------------- SGDP copy number estimates Mitchell R. Vollger, William Harvey https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/hub.txt https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/trackDb.t2t-chm13-v2.0.txt https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/bigbed/description.html download the 348 bigBeds in trackDb from https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/bigbed/ ================================================================ * encode (2022-04-26 markd) ---------------------------------------------------------------- Michael Sauria in hub https://bx.bio.jhu.edu/track-hubs/T2T/hub.txt pull from https://bx.bio.jhu.edu/track-hubs/T2T/chm13v2.0/encode/ ================================================================ * t2tRepeatMasker (2022-04-25 markd) ---------------------------------------------------------------- Savannah Hoyt, Jessica Storer, Robert Hubley http://www.repeatmasker.org/~rhubley/forMark.tar.gz chm13v2.0_RMSK_ALIGN.bb chm13v2.0_RMSK.bb combo.align.gz combo.out.gz notebook Original version was missing chrY in bigBed (find in out and align), got new one from: http://www.repeatmasker.org/~rhubley/forMark2.tar.gz rename these mv chm13v2.0_RMSK_ALIGN.bb chm13v2.0_rmsk.align.bb mv chm13v2.0_RMSK.bb chm13v2.0_rmsk.bb mv combo.align.gz chm13v2.0_rmsk.align.gz mv combo.out.gz chm13v2.0_rmsk.out.gz Track documentation was received from Savannah and updated from DFAM public hub documentation. Download images from DFAM hub, base64 encode them and insert in html/t2tRepeatMasker.html with src="data:image/png;base64,...". This makes page independent of location installed. # notes from Robert on how tracks were created: # Build trackHub tsv files from the combo* files: /home/rhubley/projects/RepeatMasker/util/rmToTrackHub2.pl \ -out combo.out \ -align combo.align # Sort tsv files sort -k1,1 -k2,2n combo.join.tsv > combo.join.tsv.sorted sort -k1,1 -k2,2n combo.align.tsv > combo.align.tsv.sorted # Convert to bigRmskBed and bigRmskAlignBed files /usr/local/ucscTools/bedToBigBed -tab -as=bigRmskAlignBed.as -type=bed3+14 combo.align.tsv.sorted chrom.sizes chm13v2.0_RMSK_ALIGN.bb /usr/local/ucscTools/bedToBigBed -tab -as=bigRmskBed.as -type=bed9+5 combo.join.tsv.sorted chrom.sizes chm13v2.0_RMSK.bb ================================================================ pending: - ensembl: http://ftp.ebi.ac.uk/pub/databases/ensembl/hprc/y1_freeze/ contains all Y1 assemblies; http://ftp.ebi.ac.uk/pub/databases/ensembl/hprc/y1_freeze/GCA_009914755.4/ is CHM13v2 - isoseq BAMs http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/out-t2t-chrY-augPB/assemblyHub/CHM13/ @PG ID:minimap2 PN:minimap2 VN:2.22-r1105-dirty CL:minimap2 -ax splice -f 1000 --sam-hit-only --secondary=no --eqx -K 100M -t 8 --cap-sw-mem=3g chm13v2.0.chrY.fasta HG002-NA24385-LCL-polished_isoforms_hq.fasta globus /HG002-IsoSeq - isoseq Fritz Sedlazeck 1 minute ago STUDY: PRJNA754107 SAMPLE: GM27730 (SAMN20741798) EXPERIMENT: PCD_NISTRM.NA27730-1_1sA-40 (SRX14226556) RUN: m64139_220130_061226 (SRR18074967) STUDY: PRJNA754107 SAMPLE: GM26105 (SAMN20741797) EXPERIMENT: PCD_NISTRM.NA26105-1_1sA-40 (SRX14226558) RUN: m64139_220131_122551 (SRR18074969) STUDY: PRJNA200694 SAMPLE: NIST HG002 NA24385 (SAMN03283347) EXPERIMENT: PCD_NISTRM.NA24385-1_1sA-40 (SRX14226557) RUN: m64139_220127_180020 (SRR18074968) * unique kmers Min unique k-mer (+) Present in v1.0 and v2.0 Michael Sauria /team-epigenetics/032522_chm13v2.0_kmers/mu/chm13v2.0.mul.bw H min_unique_kmer.html Min unique k-mer (-) Present in v1.0 and v2.0 Michael Sauria /team-epigenetics/032522_chm13v2.0_kmers/mu/chm13v2.0.mur.bw H * RepeatMasker Savannah Hoyt/Jessica Storer https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RepeatMasker_4.1.2p1.out H Robert Hubley I have generated trackhub files for the T2T TE track based on the results of Jessica's and Savannah's latest RepeatMasker runs ( 4/14/22 with v5 of the TE library ). See the notebook file for details of the construction. Please let me know if you have any questions. http://www.repeatmasker.org/~rhubley/forMark.tar.gz * ENCODE ENCODE pileups Present in v1.0 and v2.0 Michael Sauria /team-epigenetics/032522_chm13v2.0_encode/coverage/*.bw H ENCODE macs2 peaks Present in v1.0 and v2.0 Michael Sauria /team-epigenetics/032522_chm13v2.0_encode/peaks/*.bb H ENCoDE macs2 LO peaks Present in v1.0 Michael Sauria H * GRCh38 Unresolved in GRCh GRCh38 TBD Sergey Koren browser/tracks/chm13v2.0_unmapped_byHG38.bed H chm13_uncovered_byGRCh38.html GRCh37 Sergey Koren browser/tracks/chm13v2.0_unmapped_byHG19.bed H * GRCh38 variants TBD Nancy Hansen team-liftover/chain_variants/vcffiles/v1_nflo/chm13v2-grch38.sort.vcf.gz L grch_allele_differences.html GRCh37 variants TBD Nancy Hansen team-liftover/chain_variants/vcffiles/v1_nflo/chm13v2-hg19.sort.vcf.gz L * Gene GFF3/GTF downloads http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3 ================================================================ Problems: - hub groups doesn't have phenDis, so put clinvar and GWAS in varRep ================================================================