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
From: GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution
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. |