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

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Revision 207 - (hide annotations)
Wed Jan 8 15:28:47 2025 UTC (13 days, 15 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 aloraine 9 <files>
2 aloraine 96 <file name="H_sapiens_Dec_2013_ncbiRefSeqCurated.bed.gz"
3     title="RefSeq Curated"
4 nfreese 131 description="Data from UCSC Table Browser - RefSeq Curated (ncbiRefSeqCurated) table - updated Sep 23, 2020"
5 aloraine 9 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 aloraine 96 show2tracks="true"
13 aloraine 170 />
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 nfreese 131 <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 aloraine 96 url="H_sapiens_Dec_2013"
29 aloraine 100 direction_type="none"
30 aloraine 96 name_size="14"
31     label_field="id"
32 aloraine 9 background="FFFFFF"
33 aloraine 100 foreground="1B4C9B"
34 aloraine 96 show2tracks="false"
35 aloraine 207 />
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 aloraine 96 />
58 aloraine 207 <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 aloraine 9 <file name="H_sapiens_Dec_2013_all_est.psl.gz"
71 aloraine 96 title="UCSC Tracks/mRNA and EST/All human EST"
72 nfreese 131 description="Data from UCSC Table Browser - human EST alignments (all_est table) - updated Sep 30, 2020"
73 aloraine 96 url="H_sapiens_Dec_2013"
74 aloraine 9 direction_type="arrow"
75     max_depth="10"
76     name_size="16"
77     background="FFFFFF"
78     foreground="B71725"
79     label_field="id"
80 aloraine 96 show2tracks="true"
81     />
82     <file name="H_sapiens_Dec_2013_all_mrna.psl.gz"
83     title="UCSC Tracks/mRNA and EST/Human mRNAs"
84 nfreese 131 description="Data from UCSC Table Browser - human mRNA alignments (all_mrna table) - updated Sep 30, 2020"
85 aloraine 96 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 nfreese 158 <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 aloraine 9 <file name="UCSCTracks/Assembly.bed.gz"
106 aloraine 96 title="UCSC Tracks/Mapping and Sequencing/Assembly"
107 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
108 aloraine 9 />
109     <file name="UCSCTracks/Hg19_Diff.bed.gz"
110 aloraine 96 title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"
111 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
112 aloraine 9 />
113     <file name="UCSCTracks/GENCODE.bed.gz"
114 aloraine 96 title="UCSC Tracks/Genes and Gene Predictions/GENCODE"
115 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
116 aloraine 9 />
117 aloraine 99 <file name="H_sapiens_Dec_2013_ncbiRefSeq.bed.gz"
118     title="UCSC Tracks/Genes and Gene Predictions/RefSeq All"
119 nfreese 131 description="Data from UCSC Table Browser - RefSeq All (ncbiRefSeq table) - updated Sep 23, 2020"
120 aloraine 99 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 aloraine 96 <file name="H_sapiens_Dec_2013_refGene.bed.gz"
129 aloraine 98 title="UCSC Tracks/Genes and Gene Predictions/RefGene (old)"
130 nfreese 131 description="Data from UCSC Genome Browser - RefGene track, updated Sep 30, 2020"
131 aloraine 98 foreground="000000"
132     name_size="14"
133     direction_type="arrow"
134     label_field="title"
135     background="FFFFFF"
136 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
137 aloraine 96 />
138 aloraine 9 <file name="UCSCTracks/RetroGenes_V9.bed.gz"
139 aloraine 96 title="UCSC Tracks/Genes and Gene Predictions/RetroGenes V9"
140 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
141 aloraine 9 />
142     <file name="UCSCTracks/CpG_Islands.bed.gz"
143 aloraine 96 title="UCSC Tracks/Regulation/CpG Islands"
144 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
145 aloraine 9 />
146     <file name="UCSCTracks/RepeatMasker.bed.gz"
147 aloraine 96 title="UCSC Tracks/Repeats/RepeatMasker"
148 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
149 aloraine 9 />
150     <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"
151 aloraine 96 title="UCSC Tracks/Repeats/RepeatMasker Viz"
152 aloraine 106 url="H_sapiens_Dec_2013/UCSCTracks/"
153 aloraine 9 />
154 aloraine 96 <file name="cytoBand.cyt"
155     title="Cytobands"
156     load_hint="Whole Sequence"
157     />
158 aloraine 9 </files>

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