TieCov utility is meant to take the output produced by TieBrush and provide additional filtering and create additional files:
- option to write coverage data (BigWig file?) with the base coverage data
- option to write a BED junction file to represent the junction coverage data, which can be loaded by IGV as an independent junction track (the score field indicating depth of coverage) (http://software.broadinstitute.org/software/igv/splice_junctions)
The splice junction view in IGV can be loaded independent of alignments
by using a modified bed format, derived from the junctions.bed" file
produced by the TopHat program.
- this view is enabled by including a track line that specifies either
name=junctionsorst. - TopHat's "junctions.bed" file includes a track line specifying
name=junctionsby default, so no action is required for these files. - (from TopHat documentation): each junction line consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction
Example of junctions.bed file content:
track name=junctions description="TopHat junctions"
chr17_gl000205_random 36368 36643 JUNC00000003 4 + 36368 36643 255,0,0 2 21,65 0,210
chr17_gl000205_random 44994 69874 JUNC00000004 5 + 44994 69874 255,0,0 2 28,47 0,24833
chr4_gl000193_random 32293 34802 JUNC00000009 1 - 32293 34802 255,0,0 2 36,39 0,2470
chr4_gl000193_random 74344 75101 JUNC00000012 16 - 74344 75101 255,0,0 2 72,53 0,704