FADE uses BAM/SAM tags to annotate artifact reads. These tags are then used to identify and remove/clip reads.
The rs tag is a 6 bit flag that indicates read artifact status.
| Bit | Description |
|---|---|
| 0 | Read is Softclipped |
| 1 | Read's left sc is an artifact |
| 2 | Read's right sc is an artifact |
| 3 | Left Artifact aligns to mate region |
| 4 | Right Artifact aligns to mate region |
| 5 | Read has supplementary alignment |
Contains mapping information of the artifact sequence as a string: Format is CHROM, POS, CIGAR with left and right artifacts delimited by ; i.e. chr1,20,120S20M;chr1,120,15M120S
As described in our manuscript we describe an expected stem loop structure: