/[genomes]/quickload/H_sapiens_Dec_2013/annots.xml
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revision 99 by aloraine, Sun Mar 24 18:37:02 2019 UTC revision 170 by aloraine, Mon Mar 6 03:09:32 2023 UTC
# Line 1  Line 1 
1  <files>  <files>
2    <file name="H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz"    <file name="H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz"
3          title="RefSeq Curated"          title="RefSeq Curated"
4          description="Data from UCSC Table Browser - RefSeq Curated (ncbiRefSeqCurated) table - updated Mar 20, 2019"          description="Data from UCSC Table Browser - RefSeq Curated (ncbiRefSeqCurated) table - updated Sep 23, 2020"
5          url="H_sapiens_Dec_2013/"          url="H_sapiens_Dec_2013/"
6          foreground="000000"          foreground="000000"
7          name_size="14"          name_size="14"
# Line 10  Line 10 
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_snp151Common.bed.gz"    <file name="chess3.0.GRCh38.p12.bed.gz"
15          title="Genetics/Common SNPs (151)"          title="CHESS gene models v.3.0"
16          description="Data from UCSC Table Browser - common SNPs (snp151Common table) - updated Mar 20, 2019"          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            direction_type="arrow"
19          name_size="14"          name_size="14"
20          label_field="id"          label_field="id"
21          background="FFFFFF"          background="FFFFFF"
22          foreground="000000"          foreground="000000"
23            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"
32            background="FFFFFF"
33            foreground="1B4C9B"
34          show2tracks="false"          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="UCSC Tracks/mRNA and EST/All human EST"          title="UCSC Tracks/mRNA and EST/All human EST"
38          description="Data from UCSC Table Browser - human EST alignments (all_est table) - updated Mar 21, 2019"          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"
# Line 35  Line 47 
47     />     />
48      <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"      <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
49           title="UCSC Tracks/mRNA and EST/Human mRNAs"           title="UCSC Tracks/mRNA and EST/Human mRNAs"
50           description="Data from UCSC Table Browser - human mRNA alignments (all_mrna table) - updated Mar 21, 2019"           description="Data from UCSC Table Browser - human mRNA alignments (all_mrna table) - updated Sep 30, 2020"
51           url="H_sapiens_Dec_2013"           url="H_sapiens_Dec_2013"
52           direction_type="arrow"           direction_type="arrow"
53           max_depth="10"           max_depth="10"
# Line 45  Line 57 
57           label_field="id"           label_field="id"
58           show2tracks="true"           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="UCSC Tracks/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="UCSC Tracks/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="UCSC Tracks/Genes and Gene Predictions/GENCODE"          title="UCSC Tracks/Genes and Gene Predictions/GENCODE"
81            url="H_sapiens_Dec_2013/UCSCTracks/"
82     />     />
83     <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"     <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"
84           title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"           title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"
85           description="Data from UCSC Table Browser - RefSeq All (ncbiRefSeq table) - updated Mar 20, 2019"           description="Data from UCSC Table Browser - RefSeq All (ncbiRefSeq table) - updated Sep 23, 2020"
86           url="H_sapiens_Dec_2013"           url="H_sapiens_Dec_2013"
87           foreground="B71725"           foreground="B71725"
88           name_size="14"           name_size="14"
# Line 67  Line 93 
93     />     />
94     <file name="H_sapiens_Dec_2013_refGene.bed.gz"     <file name="H_sapiens_Dec_2013_refGene.bed.gz"
95          title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"          title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"
96          description="Data from UCSC Genome Browser - RefGene track, downloaded Mar 7, 2014"          description="Data from UCSC Genome Browser - RefGene track, updated Sep 30, 2020"
97          foreground="000000"          foreground="000000"
98          name_size="14"          name_size="14"
99          direction_type="arrow"          direction_type="arrow"
100          label_field="title"          label_field="title"
101          background="FFFFFF"          background="FFFFFF"
102            url="H_sapiens_Dec_2013/UCSCTracks/"
103     />     />
104     <file name="UCSCTracks/RetroGenes_V9.bed.gz"     <file name="UCSCTracks/RetroGenes_V9.bed.gz"
105          title="UCSC Tracks/Genes and Gene Predictions/RetroGenes V9"          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="UCSC Tracks/Regulation/CpG Islands"          title="UCSC Tracks/Regulation/CpG Islands"
110            url="H_sapiens_Dec_2013/UCSCTracks/"
111     />     />
112     <file name="UCSCTracks/RepeatMasker.bed.gz"     <file name="UCSCTracks/RepeatMasker.bed.gz"
113          title="UCSC Tracks/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="UCSC Tracks/Repeats/RepeatMasker Viz"          title="UCSC Tracks/Repeats/RepeatMasker Viz"
118            url="H_sapiens_Dec_2013/UCSCTracks/"
119     />     />
120     <file name="cytoBand.cyt"     <file name="cytoBand.cyt"
121           title="Cytobands"           title="Cytobands"
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