Table 2.

GOPHER output files: Seven files can be exported from GOPHER via the Export menu. These files can be used for downstream analyses, documentation, visualization, and ordering of probes. The file prefix <PREFIX> corresponds to the name of the project. The prefix of the digest file additionally contains the tag for the genome build

Filename	Description
<PREFIX>_DigestedGenome.txt	Content of lines: Coordinates, length, GC and repeat content, indication of selection, number of probes for each digest.
	Purpose: Can be used for downstream analyses.
<PREFIX>_viewPoints.tsv	Content of lines: Gene symbol, coordinates, UCSC custom URL, number of selected digests, score, length, indication whether digest with TSS is selected.
	Purpose: Documentation and sharing of results.
<PREFIX>_uniqueTargetDigests.bed	Content of lines: Coordinates and names of targeted digests. Duplicates arising from overlapping viewpoints are removed.
	Purpose: Probe design with external tools.
<PREFIX>_uniqueTargetDigestMargins.txt	Content of lines: Coordinates and names of margins of targeted digests.
	Purpose: Probe design with external tools.
<PREFIX>_allTracks.bed	Content of lines: Contains multiple sections for viewpoints, digests, margins, and probes.
	Purpose: Can be uploaded as multiple custom tracks to UCSC.
<PREFIX>_ProbeFile.bed	Content of lines: Coordinates and names of probes.
	Purpose: Ordering of probes.
<PREFIX>_agilentProbeFile.txt.zip	Content of lines: Coordinates, names, and sequences of probes.
	Purpose: Ordering of probes.