976c0e681fc3571f3a449ee2f7cb78400f11ce3e
markd
  Fri Jul 22 11:39:18 2022 -0700
moved t2t-supplied tracks out of bbi

diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt
index 8559d9d..8db7b6f 100644
--- src/hg/makeDb/doc/chm13v2.0userData/build.txt
+++ src/hg/makeDb/doc/chm13v2.0userData/build.txt
@@ -363,30 +363,36 @@
     # 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
@@ -425,19 +431,22 @@
   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
 ================================================================