RNA-Seq BAM Tags

The following BAM tags are emitted alongside spliced alignments.

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XS:A—The XS tag denotes the strand orientation of an intron. See Compatibility with Cufflinks.

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jM:B—The jM tag lists the intron motifs for all junctions in the alignments. It has the following definitions:

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0: non-canonical

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1: GT/AG

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2: CT/AC

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3: GC/AG

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4: CT/GC

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5: AT/AC

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6: GT/AT

If a gene annotations file is used during the map/align stage, and the splice junction is detected as an annotated junction, then 20 is added to its motif value.

NH:i—A standard SAM tag indicating the number of reported alignments that contains the query in the current record. This tag may be used for downstream tools such as featureCounts.

HI:i—A standard SAM tag denoting the query hit index, with its value indicating that this alignment is the i-th one stored in the SAM. Its value ranges from 1 … NH. This tag may be used for downstream tools such as featureCounts.