Setting | Description |
|---|---|
Mapping Quality >= | The Map Quality for a read must exceed this threshold for the read to map to a given location. The read can map to as many locations as where the Map Quality is met. |
Remove Ambiguous Alignments | Removes all reads that match exactly to more than one position in the reference from the analysis unless one or both of the following two options are selected: |
• If Mapping Quality is <= [ ] • Except for the Highest Map Quality Alignment | • Removes reads that match exactly to more than position only if the mapping quality is less than or equal to the indicated threshold. • Removes reads that match exactly to more than one position except for the alignment that has the highest map quality. |
Remove Paired Reads that are not Properly Paired | Removes reads that are flagged as not properly paired. The definition of “properly paired” varies among the alignment program that you used, but typically means that the both reads aligned in the correct orientation and within the expected library size. |
Match Reference | Click this option to match the reference that was used to create the BAM file with the reference that was loaded during the Load Data step for the project. See To load the reference files. |