/[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 170 - (show annotations)
Mon Mar 6 03:09:32 2023 UTC (11 months, 2 weeks ago) by aloraine
File MIME type: text/xml
File size: 4554 byte(s)
IGBF-3256 Show CHESS version 3.0 gene models for hg38
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="H_sapiens_Dec_2013_all_est.psl.gz"
37 title="UCSC Tracks/mRNA and EST/All human EST"
38 description="Data from UCSC Table Browser - human EST alignments (all_est table) - updated Sep 30, 2020"
39 url="H_sapiens_Dec_2013"
40 direction_type="arrow"
41 max_depth="10"
42 name_size="16"
43 background="FFFFFF"
44 foreground="B71725"
45 label_field="id"
46 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"
72 title="UCSC Tracks/Mapping and Sequencing/Assembly"
73 url="H_sapiens_Dec_2013/UCSCTracks/"
74 />
75 <file name="UCSCTracks/Hg19_Diff.bed.gz"
76 title="UCSC Tracks/Mapping and Sequencing/Hg19 Diff"
77 url="H_sapiens_Dec_2013/UCSCTracks/"
78 />
79 <file name="UCSCTracks/GENCODE.bed.gz"
80 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"
84 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 url="H_sapiens_Dec_2013"
87 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/RetroGenes_V9.bed.gz"
105 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"
109 title="UCSC Tracks/Regulation/CpG Islands"
110 url="H_sapiens_Dec_2013/UCSCTracks/"
111 />
112 <file name="UCSCTracks/RepeatMasker.bed.gz"
113 title="UCSC Tracks/Repeats/RepeatMasker"
114 url="H_sapiens_Dec_2013/UCSCTracks/"
115 />
116 <file name="UCSCTracks/RepeatMasker_Viz.bed.gz"
117 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>

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