GUDMAP1/GUDMAP2/nGUDMAP: Automated checking protocols - Probe Checker (Version 1.0)

Version

1.0

Notice

This page is the corresponding protocol tomestone page generated as part of the ATLAS-D2K shutdown in July 2025. Many links on this page may be broken.

Authors

Richard Baldock

Release Date

2017-09-19

Abstract

This protocol describes methods used by the Editorial Office in the University of Edinburgh for checking data entries for probes in GUDMAP1, GUDMAP2 and nGUDMAP.

Procedure

Running the Probe Checker

1. Navigate to the folder which contains both the perl script “primer_coordinates” and Blast applications.

sbms07689:~ eo$ cd Desktop/test/

Press Enter.

1. Define the path.

sbms07689:~/Desktop/test eo$ export PATH=.:$PATH

Press Enter.

1. Type “primer_coordinates” followed by the input file (text Windows format).

sbms07689:~/Desktop/test eo$ primer_coordinates ArchiveXXX.txt

Press Enter.

1. You will see something like the following: ``` Processing NM_013523.2 … Processing NM_007857.2 … Processing NM_007809.2 …

Coordinates are stored in ArchiveXXX_processed.txt

This exe file was created with the evaluation version of Perl2Exe. For more information visit http://www.indigostar.com (The full version does not display this message with a 2 second delay.) … ```

A probe report will have been generated in the “test” folder.

The filename of this report appears in the Unix shell.

(in the example above, the filename is “ArchiveXXX_processed.txt”)

IMPORTANT - The input file should contain only 3 columns. These are:

• Accession_Number
• Probe_5’
• Probe_3’

The input file must be saved as a text Windows format.

Consortium

GenitoUrinary Development Molecular Anatomy Project (GUDMAP) Consortium