Uploaded all stable, in cis multi-copy sequences and determined the genes that intersected these regions
using Galaxy tools. Built custom BED tracks to display these intervals in the UCSC Genome Browser
Galaxy File: (insert)
Dataset
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Galaxy Operation - Description
Uploaded in cis multi-copy coordinates for 3, 4, 5 copies
Uploaded in cis multi-copy coordinates for 6,7,8 copies
Uploaded in cis multi-copy coordinates for 9,10,11 copies
Uploaded in cis multi-copy coordinates for 12,13,16 copies
Uploaded in cis multi-copy coordinates for 17,18,20 copies
Uploaded in cis multi-copy coordinates for 21,22 copies
Uploaded in cis multi-copy coordinates for 23,25 copies
Uploaded in cis multi-copy coordinates for 41,42 copies
Built custom tracks for UCSC Genome Browser for all
uploaded multi-copy sequences
Uploaded stable genomic regions
Uploaded all protein-coding sequences from UCSC Table
Browser (CCDS)
Computed the lengths of protein-coding genes by subtracting
end coordinate from start coordinate
Joined protein-coding genes with stable regions to determine
which ccds genes are encoded by stable regions
Computed the lengths of each stable genomic region by
subtracting end coordinate and start coordinate
Uploaded all stable in cis multi-copy intervals
Intersected all multi-copy intervals with protein-coding genes
to determine which protein-coding genes reside in multi-copy
regions
Uploaded kgXref data from UCSC Table Browser (this data
contains gene symbols of ucsc genes)
Uploaded UCSC genes that intersect stable 3-5 multi-copy
regions
Joined UCSC gene Ids of genes that intersect 3-5 multi-copy
regions and kgXref data to determine gene symbols of genes
that intersect multi-copy regions
Uploaded UCSC genes that intersect stable 6-8 multi-copy
regions
Joined UCSC gene Ids of genes that intersect 6-8 multi-copy
regions and kgXref data to determine --> gene symbols of
genes that intersect multi-copy regions
Uploaded UCSC genes that intersect stable 9-11 multi-copy
regions
Joined UCSC gene Ids of genes that intersect 9-11 multicopy regions and kgXref data to determine --> gene symbols
of genes that intersect multi-copy regions
Uploaded UCSC genes that intersect stable 12-16 multi-copy
regions
Joined UCSC gene Ids of genes that intersect 12-16 multicopy regions and kgXref data to determine --> gene symbols
of genes that intersect multi-copy regions
Uploaded UCSC genes that intersect stable 17-20 multi-copy
regions --> result: no genes intersected these mcp regions
Galaxy Tool
Upload File
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Build custom track on data 1-8
Upload File
UCSC Main Table Browser:
ccdsGene (genome)
Compute on data 11
Join on data 10 and data 12
Compute on data 10
Upload File
Intersect on data 11 and data
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UCSC Main Table Browser:
kgXref (genome)
UCSC Main Table Browser:
knownGene (genome)
Join two Queries on data 17
and data 18
UCSC Main Table Browser:
knownGene (genome)
Join two Queries on data 17
and data 20
UCSC Main Table Browser:
knownGene (genome)
Join two Queries on data 17
and data 22
UCSC Main Table Browser:
knownGene (genome)
Join two Queries on data 17
and data 24
UCSC Main Table Browser:
knownGene (genome)
27
Uploaded UCSC genes that intersect stable 21-22 multi-copy
regions --> result: no genes intersected these mcp regions
UCSC Main Table Browser:
knownGene (genome)