--- quickload/H_sapiens_Dec_2013/annots.xml	2018/09/26 22:18:04	9
+++ quickload/H_sapiens_Dec_2013/annots.xml	2023/03/06 03:09:32	170
@@ -1,11 +1,7 @@
 <files>
-  <file name="cytoBand.cyt"
-        title="Cytobands"
-        load_hint="Whole Sequence"
-  />
-  <file name="H_sapiens_Dec_2013_refGene.bed.gz"
-        title="RefGene"
-        description="UCSC RefGene track (Mar 7, 2014)"
+  <file name="H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz"
+        title="RefSeq Curated"
+        description="Data from UCSC Table Browser - RefSeq Curated (ncbiRefSeqCurated) table - updated Sep 23, 2020"
         url="H_sapiens_Dec_2013/"
         foreground="000000"
         name_size="14"
@@ -13,57 +9,116 @@
         label_field="title"
         background="FFFFFF"
         load_hint="Whole Sequence"
-    show2tracks="true"
-  />
-  <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
-        title="mRNA"
-        description="UCSC all mRNA track (Mar 7, 2014)"
-        url="H_sapiens_Dec_2013/"
-        max_depth="10"
+        show2tracks="true"
+   />
+  <file name="chess3.0.GRCh38.p12.bed.gz"
+        title="CHESS gene models v.3.0"
+        description="Based on nearly 10,000 GTEx project RNA-Seq experiments re-formatted for IGB from chess3.0.gff.gz"
+        url="https://github.com/chess-genome/chess"
+        direction_type="arrow"
+        name_size="14"
+        label_field="id"
         background="FFFFFF"
-        foreground="B71725"
-        name_size="16"
+        foreground="000000"
+        show2tracks="true"
+   />
+  <file name="H_sapiens_Dec_2013_snp153Common.bed.gz"
+        title="Genetics/Common SNPs (153)"
+        description="Data from UCSC Table Browser - common SNPs (snp153Common table) - updated Sep 30, 2020"
+        url="H_sapiens_Dec_2013"
+        direction_type="none"
+        name_size="14"
         label_field="id"
-    show2tracks="false"/>
+        background="FFFFFF"
+        foreground="1B4C9B"
+        show2tracks="false"
+   />
   <file name="H_sapiens_Dec_2013_all_est.psl.gz"
-        title="EST"
-        description="UCSC all EST track (Mar 7, 2014)"
-        url="H_sapiens_Dec_2013/"
+        title="UCSC Tracks/mRNA and EST/All human EST"
+        description="Data from UCSC Table Browser - human EST alignments (all_est table) - updated Sep 30, 2020"
+        url="H_sapiens_Dec_2013"
         direction_type="arrow"
         max_depth="10"
         name_size="16"
         background="FFFFFF"
         foreground="B71725"
         label_field="id"
-    show2tracks="false"/>
+        show2tracks="true"
+   />
+    <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
+         title="UCSC Tracks/mRNA and EST/Human mRNAs"
+         description="Data from UCSC Table Browser - human mRNA alignments (all_mrna table) - updated Sep 30, 2020"
+         url="H_sapiens_Dec_2013"
+         direction_type="arrow"
+         max_depth="10"
+         name_size="16"
+         background="FFFFFF"
+         foreground="B71725"
+         label_field="id"
+         show2tracks="true"
+    />
+    <file name="hg38-blacklist.v2.bed.gz" 
+        title="ENCODE blacklist" 
+        description="ENCODE-identified problematic regions of the genome (hg38-blacklist.v2.bed.gz)" 
+        url="https://github.com/Boyle-Lab/Blacklist"
+        direction_type="none"
+        name_size="12"
+        background="FFFFFF"
+        foreground="000000"
+        label_field="name"
+        show2tracks="false"
+    />
    <file name="UCSCTracks/Assembly.bed.gz"
-        title="UCSCTracks/Mapping and Sequencing/Assembly"
+        title="UCSC Tracks/Mapping and Sequencing/Assembly"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
    <file name="UCSCTracks/Hg19_Diff.bed.gz"
-        title="UCSCTracks/Mapping and Sequencing/Hg19 Diff"
+        title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
    <file name="UCSCTracks/GENCODE.bed.gz"
-        title="UCSCTracks/Genes and Gene Predictions/GENCODE"
+        title="UCSC Tracks/Genes and Gene Predictions/GENCODE"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
-   <file name="UCSCTracks/RetroGenes_V9.bed.gz"
-        title="UCSCTracks/Genes and Gene Predictions/RetroGenes V9"
-   />
-   <file name="UCSCTracks/Human_mRNAs.bed.gz"
-        title="UCSCTracks/mRNA and EST/Human mRNAs"
+   <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"
+         title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"
+         description="Data from UCSC Table Browser - RefSeq All (ncbiRefSeq table) - updated Sep 23, 2020"
+         url="H_sapiens_Dec_2013"
+         foreground="B71725"
+         name_size="14"
+         direction_type="arrow"
+         label_field="title"
+         background="FFFFFF"
+         show2tracks="true"
+   />
+   <file name="H_sapiens_Dec_2013_refGene.bed.gz"
+        title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"
+        description="Data from UCSC Genome Browser - RefGene track, updated Sep 30, 2020"
+        foreground="000000"
+        name_size="14"
+        direction_type="arrow"
+        label_field="title"
+        background="FFFFFF"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
-   <file name="UCSCTracks/Spliced_ESTs.bed.gz"
-        title="UCSCTracks/mRNA and EST/Spliced ESTs"
+   <file name="UCSCTracks/RetroGenes_V9.bed.gz"
+        title="UCSC Tracks/Genes and Gene Predictions/RetroGenes V9"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
    <file name="UCSCTracks/CpG_Islands.bed.gz"
-        title="UCSCTracks/Regulation/CpG Islands"
-   />
-   <file name="UCSCTracks/Common_SNPs(142).bed.gz"
-        title="UCSCTracks/Variation/Common SNPs(142)"
+        title="UCSC Tracks/Regulation/CpG Islands"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
    <file name="UCSCTracks/RepeatMasker.bed.gz"
-        title="UCSCTracks/Repeats/RepeatMasker"
+        title="UCSC Tracks/Repeats/RepeatMasker"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
    />
    <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"
-        title="UCSCTracks/Repeats/RepeatMasker Viz"
+        title="UCSC Tracks/Repeats/RepeatMasker Viz"
+	url="H_sapiens_Dec_2013/UCSCTracks/"
+   />
+   <file name="cytoBand.cyt"
+         title="Cytobands"
+         load_hint="Whole Sequence"
    />
 </files>