GS Reads, References, FASTA and FASTQ Reads Sub-Tabs

2.6.1

To add GS read data sets to a project, click on the GS reads sub-tab, then click the Add button

to open the “Select GS Read Files” window (Figure 49). This dialog window allows you to navigate and see the available read files. Read files already in the project are visible but grayed out. You can select multiple files in this window using the ctrl or shift keys while clicking with the mouse.

Figure 49: Select GS Read Data dialog

Once the desired file(s) are selected, the “Set GS Read Data Attributes” dialog window opens. From this window (Figure 50) the GS Read files can be explicitly specified as Paired End or non-Paired End or the user can invoke auto-detection (the default setting) using the Read Type Specification dropdown. When the read type is known, it is advisable to specify it directly rather than use auto-detect as the auto-detect feature, on rare occasion, may fail to detect a Paired End file.

Figure 50: Set GS Read Data Attributes dialog

You can add any number of Read Data files to a project using the Add button, navigating to a folder, then selecting the files needed from the folder. You can even add multiple files that share the same name into a project, as long as they have different path locations in the file system (e.g. “/dir1/path1/reads.sff” and “/dir2/otherpath2/reads.sff”). In such a case, both files will be added to the Read Data list and displayed using the same name. To see the path to a file listed in the Read Data area of the main window (and the file’s last modification date), hover the mouse over the filename of interest and a tooltip containing the file’s path will be displayed. Files that have failed validation will have a red X left of the file name as an indication of failure. Pause the mouse cursor over the red X to bring up a tooltip explaining the problem encountered.

The FASTA and FASTQ Reads sub-tab is functionally similar to the GS Reads sub-tab for all project types. The only difference is that when a directory containing FASTA/FASTQ files is selected, the software examines the files in that directory to determine which files are FASTA/FASTQ files. This can take some time if there are many files in the directory, so a progress bar is displayed to show the progress of the search. See the Overview Manual, Section 2.2.2 for a discussion of the FASTQ format.

The References sub-tab is functionally similar to the Reads sub-tabs for both genomic and cDNA mapping projects. The difference is that instead of displaying all the available read data files when a directory selected, the software displays all recognized FASTA files. You may select one or more of these files. Reference files contain the DNA sequence(s) against which the reads in the Read Data files will be aligned. Once the mapping computation is run, the software determines the total number of reference sequences and bases in the file and includes this information in the two rightmost columns of the References tab (Figure 51).

Figure 51: gsMapper Project Tab References sub-tab

Although in many cases the file name extension for FASTA and FASTQ files may be .fna and .fastq, respectively, there is no standardized extension for such files. If you cannot see your FASTA/FASTQ file, try setting the “Files of Type” field to “All Files”.

Except for the Name column and the Multiplex column (which contains comma-delimited lists of the MIDs associated with the file; see Section 2.6.3, below), all columns with run statistics are initially filled with dashes (Figure 52). These data are updated in the table each time the project runs to completion. For a project that has already been through a mapping computation, summary statistics relating to the usage of the reads in the mapping process are also listed, as shown in Figure 60. On the left hand side of the reads table is a data capture buttons that can be used to capture the reads table data in csv, tab-delimited or plain or text formats.

Figure 52: Project Tab of the gsMapper (GS Reads sub-tab)