/[genomes]/quickload/H_sapiens_Dec_2013/annots.xml
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revision 9 by aloraine, Wed Sep 26 22:18:04 2018 UTC revision 170 by aloraine, Mon Mar 6 03:09:32 2023 UTC
# Line 1  Line 1 
1  <files>  <files>
2    <file name="cytoBand.cyt"    <file name="H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz"
3          title="Cytobands"          title="RefSeq Curated"
4          load_hint="Whole Sequence"          description="Data from UCSC Table Browser - RefSeq Curated (ncbiRefSeqCurated) table - updated Sep 23, 2020"
   />  
   <file name="H_sapiens_Dec_2013_refGene.bed.gz"  
         title="RefGene"  
         description="UCSC RefGene track (Mar 7, 2014)"  
5          url="H_sapiens_Dec_2013/"          url="H_sapiens_Dec_2013/"
6          foreground="000000"          foreground="000000"
7          name_size="14"          name_size="14"
# Line 13  Line 9 
9          label_field="title"          label_field="title"
10          background="FFFFFF"          background="FFFFFF"
11          load_hint="Whole Sequence"          load_hint="Whole Sequence"
12      show2tracks="true"          show2tracks="true"
13    />     />
14    <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"    <file name="chess3.0.GRCh38.p12.bed.gz"
15          title="mRNA"          title="CHESS gene models v.3.0"
16          description="UCSC all mRNA track (Mar 7, 2014)"          description="Based on nearly 10,000 GTEx project RNA-Seq experiments re-formatted for IGB from chess3.0.gff.gz"
17          url="H_sapiens_Dec_2013/"          url="https://github.com/chess-genome/chess"
18          max_depth="10"          direction_type="arrow"
19            name_size="14"
20            label_field="id"
21          background="FFFFFF"          background="FFFFFF"
22          foreground="B71725"          foreground="000000"
23          name_size="16"          show2tracks="true"
24       />
25      <file name="H_sapiens_Dec_2013_snp153Common.bed.gz"
26            title="Genetics/Common SNPs (153)"
27            description="Data from UCSC Table Browser - common SNPs (snp153Common table) - updated Sep 30, 2020"
28            url="H_sapiens_Dec_2013"
29            direction_type="none"
30            name_size="14"
31          label_field="id"          label_field="id"
32      show2tracks="false"/>          background="FFFFFF"
33            foreground="1B4C9B"
34            show2tracks="false"
35       />
36    <file name="H_sapiens_Dec_2013_all_est.psl.gz"    <file name="H_sapiens_Dec_2013_all_est.psl.gz"
37          title="EST"          title="UCSC Tracks/mRNA and EST/All human EST"
38          description="UCSC all EST track (Mar 7, 2014)"          description="Data from UCSC Table Browser - human EST alignments (all_est table) - updated Sep 30, 2020"
39          url="H_sapiens_Dec_2013/"          url="H_sapiens_Dec_2013"
40          direction_type="arrow"          direction_type="arrow"
41          max_depth="10"          max_depth="10"
42          name_size="16"          name_size="16"
43          background="FFFFFF"          background="FFFFFF"
44          foreground="B71725"          foreground="B71725"
45          label_field="id"          label_field="id"
46      show2tracks="false"/>          show2tracks="true"
47       />
48        <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
49             title="UCSC Tracks/mRNA and EST/Human mRNAs"
50             description="Data from UCSC Table Browser - human mRNA alignments (all_mrna table) - updated Sep 30, 2020"
51             url="H_sapiens_Dec_2013"
52             direction_type="arrow"
53             max_depth="10"
54             name_size="16"
55             background="FFFFFF"
56             foreground="B71725"
57             label_field="id"
58             show2tracks="true"
59        />
60        <file name="hg38-blacklist.v2.bed.gz"
61            title="ENCODE blacklist"
62            description="ENCODE-identified problematic regions of the genome (hg38-blacklist.v2.bed.gz)"
63            url="https://github.com/Boyle-Lab/Blacklist"
64            direction_type="none"
65            name_size="12"
66            background="FFFFFF"
67            foreground="000000"
68            label_field="name"
69            show2tracks="false"
70        />
71     <file name="UCSCTracks/Assembly.bed.gz"     <file name="UCSCTracks/Assembly.bed.gz"
72          title="UCSCTracks/Mapping and Sequencing/Assembly"          title="UCSC Tracks/Mapping and Sequencing/Assembly"
73            url="H_sapiens_Dec_2013/UCSCTracks/"
74     />     />
75     <file name="UCSCTracks/Hg19_Diff.bed.gz"     <file name="UCSCTracks/Hg19_Diff.bed.gz"
76          title="UCSCTracks/Mapping and Sequencing/Hg19 Diff"          title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"
77            url="H_sapiens_Dec_2013/UCSCTracks/"
78     />     />
79     <file name="UCSCTracks/GENCODE.bed.gz"     <file name="UCSCTracks/GENCODE.bed.gz"
80          title="UCSCTracks/Genes and Gene Predictions/GENCODE"          title="UCSC Tracks/Genes and Gene Predictions/GENCODE"
81            url="H_sapiens_Dec_2013/UCSCTracks/"
82     />     />
83     <file name="UCSCTracks/RetroGenes_V9.bed.gz"     <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"
84          title="UCSCTracks/Genes and Gene Predictions/RetroGenes V9"           title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"
85     />           description="Data from UCSC Table Browser - RefSeq All (ncbiRefSeq table) - updated Sep 23, 2020"
86     <file name="UCSCTracks/Human_mRNAs.bed.gz"           url="H_sapiens_Dec_2013"
87          title="UCSCTracks/mRNA and EST/Human mRNAs"           foreground="B71725"
88             name_size="14"
89             direction_type="arrow"
90             label_field="title"
91             background="FFFFFF"
92             show2tracks="true"
93       />
94       <file name="H_sapiens_Dec_2013_refGene.bed.gz"
95            title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"
96            description="Data from UCSC Genome Browser - RefGene track, updated Sep 30, 2020"
97            foreground="000000"
98            name_size="14"
99            direction_type="arrow"
100            label_field="title"
101            background="FFFFFF"
102            url="H_sapiens_Dec_2013/UCSCTracks/"
103     />     />
104     <file name="UCSCTracks/Spliced_ESTs.bed.gz"     <file name="UCSCTracks/RetroGenes_V9.bed.gz"
105          title="UCSCTracks/mRNA and EST/Spliced ESTs"          title="UCSC Tracks/Genes and Gene Predictions/RetroGenes V9"
106            url="H_sapiens_Dec_2013/UCSCTracks/"
107     />     />
108     <file name="UCSCTracks/CpG_Islands.bed.gz"     <file name="UCSCTracks/CpG_Islands.bed.gz"
109          title="UCSCTracks/Regulation/CpG Islands"          title="UCSC Tracks/Regulation/CpG Islands"
110     />          url="H_sapiens_Dec_2013/UCSCTracks/"
    <file name="UCSCTracks/Common_SNPs(142).bed.gz"  
         title="UCSCTracks/Variation/Common SNPs(142)"  
111     />     />
112     <file name="UCSCTracks/RepeatMasker.bed.gz"     <file name="UCSCTracks/RepeatMasker.bed.gz"
113          title="UCSCTracks/Repeats/RepeatMasker"          title="UCSC Tracks/Repeats/RepeatMasker"
114            url="H_sapiens_Dec_2013/UCSCTracks/"
115     />     />
116     <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"     <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"
117          title="UCSCTracks/Repeats/RepeatMasker Viz"          title="UCSC Tracks/Repeats/RepeatMasker Viz"
118            url="H_sapiens_Dec_2013/UCSCTracks/"
119       />
120       <file name="cytoBand.cyt"
121             title="Cytobands"
122             load_hint="Whole Sequence"
123     />     />
124  </files>  </files>
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