We used Galaxy to retrieve FASTA sequences of single-copy (sc-) stable intervals. Subsequently, these
sequences were used in mpiBLAST for determining multi-copy stable intervals. This is a Galaxy history
for chromosome 18 as an example of the workflow used for retrieving sc-stable sequences for all
autosomes.
Galaxy File: (insert)
Dataset
1
2
Dataset Description
Uploaded stable regions
Uploaded repeat masker file from UCSC
3
Uploaded segmental duplication track from UCSC
4
Filtered data by chromosome of interest
Subtracted repeats from all stable regions --> result:
list of single copy (sc) stable intervals
Determined sc-stable intervals having segmental
duplicons by performing an intersection
Determined if there are any overlapping intervals
that have segmental duplicons
Subtracted clustered sc-stable intervals with
segmental duplications - to return NON-overlapping
intervals that have segmental duplications
Formatted the list of sc-stable intervals having
segmental duplications
Computed a subtraction: column3 - column2 to
determine the length of the sc-stable intervals
Filtered the results by keeping intervals having
length of >500bp
Extract FASTA sequence files for each sc-stable
interval (hg16 assembly)
Converted genomic coordinates of sc-stable
intervals (>500bp) to hg18 assembly
Extracted FASTA sequences for each sc-stable
interval (>500bp) hg18
Re-filtered the data by length of sc-stable interval:
by >100bp
Converted all sc-stable intervals to hg18 assembly
(>100bp)
This determined how many and which sc-stable
intervals (>100bp and <500bp) were not used in
mpiBLAST search (as only >500bp intervals were
used)
5
6
7
8
9
10
11
12
13-14
15
16
17-18
19
Galaxy Tool
Upload File
UCSC Main Table Browser: rmsk
UCSC Main Table Browser:
genomicSuperDups
Filter on data 3
Subtract on data 1 and data 2
Intersect on data 4 and data 5
Cluster on data 6
Subtract on data 6 and data 7
Cut on data 8
Compute on data 9
Filter on data 10
Extract Genomic DNA on data 11
Convert genome coordinates on data 11
Extract Genomic DNA on data 14
Filter on data 10
Convert genome coordinates on data 16
Join on data 14 and data 18