User guide

Introduction

AgileSamFileMerger merges two or more ordered *.sam files into a single ordered *.sam file.

Note: During the ordering process, the working directory may contain a copy both of the original files and of the merged *.sam file; consequently, it is important to perform the task on a hard disk with plenty of free space. Also, since AgileSamFileMerger reads and writes a large amount of data, the sorting should be performed on a local hard disk. If the original unsorted *.sam file is on a network drive or a USB stick, the sorting process may take a VERY long time to complete.

Merging a number of SAM files

To merge a number of sorted *.sam files, press the Select button and pick the folder containing the sorted *.sam files to be combined. Next press Save as and enter the name of the file to export the data to. Finally, click the Create button. During the merging process, the number of exported sequences is displayed in the program’s title bar (Figure 1). Only correctly formatted sequences that have been aligned to the reference sequence are exported. If the sorted *.sam file is to be used on a Linux or Apple computer select the Linux line break option (Figure 2).

During the merging process, the working directory may contain twice as much data as the original sorted *.sam files, so it is important to merge data on a disk with plenty of free space.

Figure 1: During the merging process
AgileSamFileMerger displays the number of
exported sequences in its title bar.

Figure 2: The Linux option creates
files with Linux compatible line breaks.