From Array Suite Wiki
Add Mapped DNA-SeQ Reads
The Add Mapped DNA-Seq Reads module allows the user to import DNA-Seq data aligned outside of Omicsoft and return a number of summary statistics and an NGS dataset (used for further downstream analysis like mutation generation, , paired fusion gene detection, and more).
This module supports the BAM and SAM file formats for input files.
- The Filter section allows the user to filter by particular sequences or regions, or import all reads from the file into the software.
- The Reference library for mapping must be selected (including anywhere an index has already been built, and allows the user to build one on the fly for a new Genome).
- The user can choose to either include, ignore, or throw an error for unmapped reads found in the imported file.
- The user can choose to name the output file.
- Do not copy sorted BAM files - Having this option selected (default) will prevent the sorted BAM files from being copied into the local project directory.
The resulting files could include an alignment summary table and the NGS dataset (for downstream analysis like creation of mutation data, fusion data, etc.