6391bfb6e9dfe4e7a408bb48ce36c85349766c46
markd
  Tue Apr 26 18:53:38 2022 -0700
added CHM13 ENCODE tracks

diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt
index 6d3a109..e35d235 100644
--- src/hg/makeDb/doc/chm13v2.0userData/build.txt
+++ src/hg/makeDb/doc/chm13v2.0userData/build.txt
@@ -309,30 +309,41 @@
 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/
+
+
+	ENCODE	ENCODE pileups	Ready: See hub.txt	Michael Sauria			https://bx.bio.jhu.edu/track-hubs/T2T/hub.txt	H
+		ENCODE macs2 peaks		Michael Sauria				H
+		ENCODE macs2 LO peaks		Michael Sauria				H
 
 ================================================================
 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