/[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 207 by aloraine, Wed Jan 8 15:28:47 2025 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"
35        />
36        <file name="https://data.bioviz.org/genomeseq/H_sapiens_Dec_2013/M1YNF4X1J.cram"
37            index="https://data.bioviz.org/genomeseq/H_sapiens_Dec_2013/M1YNF4X1J.cram.crai"
38            title="Genetics/Individual/Donor 1 M1YNF4X1J"
39            description="Donor 1 whole genome sequencing read alignment results from Nebula Genomics"
40            direction_type="none"
41            name_size="14"
42            max_depth="10"
43            background="FFFFFF"
44            foreground="1B4C9B"
45          show2tracks="false"          show2tracks="false"
46        />
47        <file name="https://data.bioviz.org/genomeseq/unknown_reference/SQ867JX4-30x-WGS-Sequencing_com-12-25-24.bam"
48            index="https://data.bioviz.org/genomeseq/unknown_reference/SQ867JX4-30x-WGS-Sequencing_com-12-25-24.bam.bai"
49            title="Genetics/Individual/Donor 1 SQ867JX4"
50            description="Donor 1 whole genome sequencing read alignment results from Sequencing.com"
51            direction_type="none"
52            name_size="14"
53            max_depth="10"
54            background="FFFFFF"
55            foreground="1B4C9B"
56            show2tracks="false"
57       />
58      <file name="https://e4d05c260dbc25ea5821e03eb009a2b7-26238.collections.ac2it.arvadosapi.com/_/NB72462M.cram"
59            index="https://data.cyverse.org/dav-anon/iplant/home/nowlanf/cram/index/NB72462M.cram.crai"
60            title="Genetics/Individual/NB72462M - Personal Genome Project"
61            description="Whole genome sequencing read alignments from participant huF7A4DE file NB72462M.cram"
62            direction_type="none"
63            name_size="14"
64            max_depth="10"
65            background="FFFFFF"
66            foreground="1B4C9B"
67            show2tracks="false"
68            url="https://my.pgp-hms.org/profile/huF7A4DE"
69     />     />
70    <file name="H_sapiens_Dec_2013_all_est.psl.gz"    <file name="H_sapiens_Dec_2013_all_est.psl.gz"
71          title="UCSC Tracks/mRNA and EST/All human EST"          title="UCSC Tracks/mRNA and EST/All human EST"
72          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"
73          url="H_sapiens_Dec_2013"          url="H_sapiens_Dec_2013"
74          direction_type="arrow"          direction_type="arrow"
75          max_depth="10"          max_depth="10"
# Line 35  Line 81 
81     />     />
82      <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"      <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
83           title="UCSC Tracks/mRNA and EST/Human mRNAs"           title="UCSC Tracks/mRNA and EST/Human mRNAs"
84           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"
85           url="H_sapiens_Dec_2013"           url="H_sapiens_Dec_2013"
86           direction_type="arrow"           direction_type="arrow"
87           max_depth="10"           max_depth="10"
# Line 45  Line 91 
91           label_field="id"           label_field="id"
92           show2tracks="true"           show2tracks="true"
93      />      />
94        <file name="hg38-blacklist.v2.bed.gz"
95            title="ENCODE blacklist"
96            description="ENCODE-identified problematic regions of the genome (hg38-blacklist.v2.bed.gz)"
97            url="https://github.com/Boyle-Lab/Blacklist"
98            direction_type="none"
99            name_size="12"
100            background="FFFFFF"
101            foreground="000000"
102            label_field="name"
103            show2tracks="false"
104        />
105     <file name="UCSCTracks/Assembly.bed.gz"     <file name="UCSCTracks/Assembly.bed.gz"
106          title="UCSC Tracks/Mapping and Sequencing/Assembly"          title="UCSC Tracks/Mapping and Sequencing/Assembly"
107            url="H_sapiens_Dec_2013/UCSCTracks/"
108     />     />
109     <file name="UCSCTracks/Hg19_Diff.bed.gz"     <file name="UCSCTracks/Hg19_Diff.bed.gz"
110          title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"          title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"
111            url="H_sapiens_Dec_2013/UCSCTracks/"
112     />     />
113     <file name="UCSCTracks/GENCODE.bed.gz"     <file name="UCSCTracks/GENCODE.bed.gz"
114          title="UCSC Tracks/Genes and Gene Predictions/GENCODE"          title="UCSC Tracks/Genes and Gene Predictions/GENCODE"
115            url="H_sapiens_Dec_2013/UCSCTracks/"
116     />     />
117     <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"     <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"
118           title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"           title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"
119           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"
120           url="H_sapiens_Dec_2013"           url="H_sapiens_Dec_2013"
121           foreground="B71725"           foreground="B71725"
122           name_size="14"           name_size="14"
# Line 67  Line 127 
127     />     />
128     <file name="H_sapiens_Dec_2013_refGene.bed.gz"     <file name="H_sapiens_Dec_2013_refGene.bed.gz"
129          title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"          title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"
130          description="Data from UCSC Genome Browser - RefGene track, downloaded Mar 7, 2014"          description="Data from UCSC Genome Browser - RefGene track, updated Sep 30, 2020"
131          foreground="000000"          foreground="000000"
132          name_size="14"          name_size="14"
133          direction_type="arrow"          direction_type="arrow"
134          label_field="title"          label_field="title"
135          background="FFFFFF"          background="FFFFFF"
136            url="H_sapiens_Dec_2013/UCSCTracks/"
137     />     />
138     <file name="UCSCTracks/RetroGenes_V9.bed.gz"     <file name="UCSCTracks/RetroGenes_V9.bed.gz"
139          title="UCSC Tracks/Genes and Gene Predictions/RetroGenes V9"          title="UCSC Tracks/Genes and Gene Predictions/RetroGenes V9"
140            url="H_sapiens_Dec_2013/UCSCTracks/"
141     />     />
142     <file name="UCSCTracks/CpG_Islands.bed.gz"     <file name="UCSCTracks/CpG_Islands.bed.gz"
143          title="UCSC Tracks/Regulation/CpG Islands"          title="UCSC Tracks/Regulation/CpG Islands"
144            url="H_sapiens_Dec_2013/UCSCTracks/"
145     />     />
146     <file name="UCSCTracks/RepeatMasker.bed.gz"     <file name="UCSCTracks/RepeatMasker.bed.gz"
147          title="UCSC Tracks/Repeats/RepeatMasker"          title="UCSC Tracks/Repeats/RepeatMasker"
148            url="H_sapiens_Dec_2013/UCSCTracks/"
149     />     />
150     <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"     <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"
151          title="UCSC Tracks/Repeats/RepeatMasker Viz"          title="UCSC Tracks/Repeats/RepeatMasker Viz"
152            url="H_sapiens_Dec_2013/UCSCTracks/"
153     />     />
154     <file name="cytoBand.cyt"     <file name="cytoBand.cyt"
155           title="Cytobands"           title="Cytobands"
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