GS Reporter output

2. GS Reporter : 2.2 GS Reporter output

2.2	GS Reporter output

2.2.1 GS Reporter Metrics Files

2.2.2 GS Reporter FNA and QUAL Files

2.2.3 Organization of a Data Processing Directory

The default output files of the gsReporter application are the following:

•	454RuntimeMetricsAll.txt/.csv

•	region.key.454RuntimeMetrics.txt/.csv

•	454QualityFilterMetrics.txt/.csv

•	454BaseCallerMetrics.txt/.csv

•	454AllControlMetrics.txt/.csv

•	region.librarykey.454Reads.fna

•	region.librarykey.454Reads.qual

where ’.txt/.csv’ denotes that both tab-delimited (*.txt) and comma-delimited (*.csv) files are output, and ‘region.key.’ denotes that one file per region-key combination is output.

The .fna and .qual files for the Control DNA reads are no longer automatically generated by the default gsReporter options but can generated by using the following constructs:

gsReporter --fna=control 1.cwf, or gsReporter --qual=TCAG 1.cwf

The ‘454AllControlMetrics.txt’ file contains the summary statistics for the Control DNA metrics and is useful in situations in which multiple control keys are used in a Run (see Section 7.1 for more details on this). It is generated by default, but is not generated when using the --legacy option to gsReporter.