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Using custom SAM tags with TALON
Dana Wyman edited this page Mar 20, 2020
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TALON recognizes and stores the following custom SAM tags in the observed table of the database on a per-read basis. The values of these tags are also reported in the read_annot output file.
| Tag | Type | Description |
|---|---|---|
| fA:f | float | Fraction As in post-alignment window |
| lC:Z | string | Custom label |
| lA:Z | string | Allelic label |
| tS:Z | string | Transcript start support |
| tE:Z | string | Transcript end support |
Currently, only one of these tags is in active use by the TALON pipeline, namely the fA tag for internal priming detection. We added the lA, tS, and tE tags to help support features in the future such as allele-based quantification or more sophisticated transcript filtering. The custom lC tag is intended to allow users to record SAM information of their choice to pass into TALON.