HD probe searches, SNP probe searches, Genomic Tiling, and Bait Tiling
can use genomic intervals as parameters. You can use Interval Finder to
produce a list of genomic intervals that can be used with these tools
that are associated with specific annotations. Interval Finder is available
for the CGH, ChIP, SureSelect Capture Array, SureSelect Target Enrichment,
and SureSelect RNA Enrichment application types.
Option |
Instructions/Details |
All |
This type of search returns intervals that have any
annotation that matches a single search term that you enter.
In Search Term(s), type the desired term.
By default,
eArray returns intervals that contain the search term within any associated
annotation. To limit returned intervals to those whose annotation matches
the search term exactly, mark Exact Search.
|
Accessions |
In Search Term(s),
type an accession number, without its source, or multiple accession numbers
separated by pipe "|" characters. The search returns the genomic
intervals that correspond with each of the accessions. For the search
to return intervals, accessions must match exactly. Use upper case (capital)
letters in accessions.
Example:
NM_012257|Q0055|NM_012298
You can also upload a file of accessions. Prepare
a plain text file with an extension of .txt. Put one accession on each
line, and end each line with a new line
character (press Enter). To upload
the file, click Upload. For details,
see Upload data for probe
searches. |
Cytoband |
In Search Term(s),
type a cytoband designation, without its source, or multiple cytobands
separated by pipe "|" characters. The search returns the genomic
intervals that correspond with each of the cytobands. For the search to
return intervals, cytobands must match exactly. Use lower case letters
to specify the p or q chromosome arms.
Example:
1p22.2|2q33.3
You can also upload a file of cytobands. Prepare
a plain text file with an extension of .txt. List one cytoband per line,
and end each line with a new line
character (press Enter). To upload
the file, click Upload. For details,
see Upload data for probe
searches. |
Gene Symbol |
In Search Term(s),
type a gene symbol, or multiple gene symbols separated by pipe "|"
characters. The search returns the genomic intervals that correspond with
each of the gene symbols. For the search to return intervals, gene symbols
must match exactly. Use upper case (capital) letters in gene symbols.
Example:
H3N2|BRMS1|BRCA1
You can also upload a file of gene symbols. Prepare
a plain text file with an extension of .txt. List one gene symbol per
line, and end each line with a new line
character (press Enter). To upload
the file, click Upload. For details,
see Upload data for probe
searches. |
After eArray displays the retrieved genomic
intervals, you can take action on them.
Task |
Instructions/Details |
Select a single interval |
Mark the check box in its row. |
Select additional intervals |
Mark the check boxes next to the name of each desired
interval.
eArray remembers your selections if you navigate to different pages. |
Go to another page of Search
Results |
Click the Pages
links. eArray remembers your selections as you go from page to page. |
Sort the results |
Click the heading of a column.
eArray sorts the results based on the contents of the given column. To
reverse the order of the items in the list, click the heading again. |
Select all intervals on
all pages |
Mark Select Entire
Result. |
Select all intervals on
one page |
Mark the check box in the column heading row. |
Task |
Instructions/Details |
Download the selected intervals
as a list |
Click Download.
A progress message appears, and a File Download dialog box opens.
Click Save.
A Save As dialog box appears.
Select a location for the downloaded file, then
click Save.
eArray downloads the intervals in ZIP format. The ZIP archive contains
a single *.tdt file that has one interval on each line.
|
Download the selected intervals
as a BED format file |
This task can be useful
if you want to use the selected intervals in a genome browser or other
software that accepts BED format files.
Click
Download in BED Format.
A progress message appears, and a File Download dialog box opens.
Click
Save.
A Save As dialog box appears.
Select
a location for the downloaded file, then click Save.
eArray downloads the intervals in ZIP format. The ZIP archive contains
a single *.tdt file that has one interval on each line. The file contains
only the genomic coordinates of the selected intervals.
|
Start a new HD search based
on the selected intervals |
(CGH and ChIP application
types)
Click Run HD
Search.
The Standard Genomic Intervals HD Search page appears. The selected
intervals appear in pipe-separated format in Genomic Intervals.
Set the other search parameters, as needed,
then click Search. See
|
Start a Genomic Tiling
job based on the selected intervals |
(SureSelect Capture Array
application type)
Click Run Genomic
Tiling.
The Genomic Tiling page appears. The selected intervals appear in pipe-separated
format in Genomic Intervals.
Set the other Genomic Tiling parameters, as
needed, then click Submit. See
Set up a Genomic Tiling job.
Note:
To use retrieved intervals for a Genomic Tiling job in the CGH and ChIP
application types, download the intervals. When you set up the Genomic
Tiling job, upload them in the Genomic Intervals tiling parameter.
|
Start a Bait Tiling job
based on the selected intervals |
(SureSelect Target Enrichment
and SureSelect RNA Enrichment application types)
Click Run Bait
Tiling.
The Bait Tiling page appears. The selected intervals appear in pipe-separated
format in Genomic Target Intervals.
Set the other Bait Tiling parameters, as needed,
then click Submit. See Bait Tiling (SureSelect Target Enrichment)
and Bait
Tiling (SureSelect RNA Enrichment).
|
Start a SNP probe search
based on the selected intervals |
(CGH application type)
Download the selected intervals,
as described at the top of this table, then upload them in the Genomic
Intervals parameter. See Search for
SNP probes. |
Download a list of the
search terms that did not return any intervals |
Click Download
Unfound Terms.
A progress message appears, and a File Download dialog box opens.
Click Save.
A Save As dialog box appears.
Select a location for the downloaded file, then
click Save.
eArray downloads the intervals in ZIP format. The ZIP archive contains
a single *.tdt file that has one unfound term on each line.
|
View a list of the chromosomes
associated with the selected intervals |
|