NOTE: this respository is deprecated and no longer maintained for public use (though occasional testing of some development features may still take place here), please use https://github.com/alevar/tiebrush instead, as the official, current repository for TieBrush software.
- YC:i:N stores the number of alignments that were merged into this alignment record (multiplicity count)
- YX:i:N stores the number of samples that have this alignment (sample count)
If either of these tags are missing (i.e. GBamRecord::tag_int() call returns 0) then the alignment is unique (when YC is 0) or only one sample has it (if YX is 0). The actual count in these cases is obviously 1.
In an attempt to reflect a measure of "mosaicity" for read alignments in a sample, the following tag is also added :
- YD:i:N keeps track of the maximum number of contiguous bases preceding the start of the read alignment in the samples(s) that it belongs to. In other words, if the current alignment is part of an exon-overlapping bundle (strand specific!), this value holds the maximum distance from the beginning of the bundle to the start of this alignment, across all samples having this alignment. If the alignment is not in a bundle (i.e. it is preceded by a uncovered region as it is not overlapped by any another alignment with a lower start position), in all the individual samples where that alignment is present, then the YD value is 0 and the tag is omitted from the output file produced by TieBrush. That means that all the alignments lacking a YD tag in the TieBrush output start at the very beginning of an exon-overlapping bundle (i.e. are not overlapped by a preceding alignment with a lower start coordinate).
The tiecov utility can take the output file produced by TieBrush and can generate the following auxiliary base/junction coverage files:
- a BedGraph file with the coverage data (see http://genome.ucsc.edu/goldenPath/help/bedgraph.html); this file can be converted to BigWig (using bedGraphToBigWig) or to TDF format (using igvtools) in order to be loaded in IGV as an additional coverage track
- a junction BED file which can be loaded directly in IGV as an additional junction track (http://software.broadinstitute.org/software/igv/splice_junctions)