4492d656288371cb1802c3a38217acb11bde6368 markd Thu Jun 15 11:45:05 2023 -0700 removed obsolete attempt to integrate CHM13 with GenArk diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt deleted file mode 100644 index 8db7b6f..0000000 --- src/hg/makeDb/doc/chm13v2.0userData/build.txt +++ /dev/null @@ -1,452 +0,0 @@ -================================================================ -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=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 - -2022-05-23 -# due to the number of problems with the bigRmsk code, we are temporarily converting it to -# a bigBed and added colors. - - cd /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/trackData/t2tRepeatMasker - bigBedToBed chm13v2.0_rmsk.align.bb stdout | awk -f addItemRgb.awk >chm13v2.0_rmsk.align.rgb.bed - -================================================================ -2022-07-21 methylationFreq -================================================================ -Methylation Frequency (Paul Hook & Ariel Gershman ) - -https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/regulation/chm13v2.0_CpG_methylationFrequency.bw - -================================================================ -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 -================================================================