You use the Export Sequences tool to generate a .fasta file that contains all the reads that aligned to a specific region in the reference sequence. You can manually set the region length (which means that you must specify the starting position and the ending position), or you can upload a Comma-delimited text file or a tab-delimited text file that is in a BED file format.

Optionally, after you specify the settings for the Export Sequences tool, you can click Save Settings to save the settings to a Settings (.ini) file. You can select this saved general Settings file for post-processing options in: