/[genomes]/quickload/H_sapiens_Dec_2013/annots.xml
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Contents of /quickload/H_sapiens_Dec_2013/annots.xml

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Revision 207 - (show annotations)
Wed Jan 8 15:28:47 2025 UTC (13 days, 12 hours ago) by aloraine
File MIME type: text/xml
File size: 6134 byte(s)
IGBF-3748 Share Donor 1 sequence alignments from sequencing.com and NebulaGenomics and for person huF7A4DE in personal genomics project
1 <files>
2 <file name="H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz"
3 title="RefSeq Curated"
4 description="Data from UCSC Table Browser - RefSeq Curated (ncbiRefSeqCurated) table - updated Sep 23, 2020"
5 url="H_sapiens_Dec_2013/"
6 foreground="000000"
7 name_size="14"
8 direction_type="arrow"
9 label_field="title"
10 background="FFFFFF"
11 load_hint="Whole Sequence"
12 show2tracks="true"
13 />
14 <file name="chess3.0.GRCh38.p12.bed.gz"
15 title="CHESS gene models v.3.0"
16 description="Based on nearly 10,000 GTEx project RNA-Seq experiments re-formatted for IGB from chess3.0.gff.gz"
17 url="https://github.com/chess-genome/chess"
18 direction_type="arrow"
19 name_size="14"
20 label_field="id"
21 background="FFFFFF"
22 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"
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"
71 title="UCSC Tracks/mRNA and EST/All human EST"
72 description="Data from UCSC Table Browser - human EST alignments (all_est table) - updated Sep 30, 2020"
73 url="H_sapiens_Dec_2013"
74 direction_type="arrow"
75 max_depth="10"
76 name_size="16"
77 background="FFFFFF"
78 foreground="B71725"
79 label_field="id"
80 show2tracks="true"
81 />
82 <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
83 title="UCSC Tracks/mRNA and EST/Human mRNAs"
84 description="Data from UCSC Table Browser - human mRNA alignments (all_mrna table) - updated Sep 30, 2020"
85 url="H_sapiens_Dec_2013"
86 direction_type="arrow"
87 max_depth="10"
88 name_size="16"
89 background="FFFFFF"
90 foreground="B71725"
91 label_field="id"
92 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"
106 title="UCSC Tracks/Mapping and Sequencing/Assembly"
107 url="H_sapiens_Dec_2013/UCSCTracks/"
108 />
109 <file name="UCSCTracks/Hg19_Diff.bed.gz"
110 title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"
111 url="H_sapiens_Dec_2013/UCSCTracks/"
112 />
113 <file name="UCSCTracks/GENCODE.bed.gz"
114 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"
118 title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"
119 description="Data from UCSC Table Browser - RefSeq All (ncbiRefSeq table) - updated Sep 23, 2020"
120 url="H_sapiens_Dec_2013"
121 foreground="B71725"
122 name_size="14"
123 direction_type="arrow"
124 label_field="title"
125 background="FFFFFF"
126 show2tracks="true"
127 />
128 <file name="H_sapiens_Dec_2013_refGene.bed.gz"
129 title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"
130 description="Data from UCSC Genome Browser - RefGene track, updated Sep 30, 2020"
131 foreground="000000"
132 name_size="14"
133 direction_type="arrow"
134 label_field="title"
135 background="FFFFFF"
136 url="H_sapiens_Dec_2013/UCSCTracks/"
137 />
138 <file name="UCSCTracks/RetroGenes_V9.bed.gz"
139 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"
143 title="UCSC Tracks/Regulation/CpG Islands"
144 url="H_sapiens_Dec_2013/UCSCTracks/"
145 />
146 <file name="UCSCTracks/RepeatMasker.bed.gz"
147 title="UCSC Tracks/Repeats/RepeatMasker"
148 url="H_sapiens_Dec_2013/UCSCTracks/"
149 />
150 <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"
151 title="UCSC Tracks/Repeats/RepeatMasker Viz"
152 url="H_sapiens_Dec_2013/UCSCTracks/"
153 />
154 <file name="cytoBand.cyt"
155 title="Cytobands"
156 load_hint="Whole Sequence"
157 />
158 </files>

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