In this tutorial, you will learn how to interpret the read pileup plots generated by TRGT.
- Create allele plots that depict repeat alleles and reads aligning to them
(
--plot-type allele, default). - Create waterfall plots that depict portions of HiFi reads spanning the repeat
without aligning them (
--plot-type waterfall). The waterfall plots are especially convenient for visualizing mosaicism. - Color code the repeat structure on allele and waterfall plots
(
--show motifs, default). - Display 5mCpG methylation levels on allele and waterfall plots (
--show meth).
In the remainder of this document we will go over examples of TRGT plots.
This example concerns a repeat region in the HTT gene. This region contains two tandem repeats, one consists of CAGs and the other consists of CCGs. The expansions of the CAG repeat are known to cause Huntington's disease.
The allele plot below consists of two panels, each corresponding to a haplotype of this region. The first track of each panel depicts the haplotype consensus sequence. The CAG and CCG repeats are shown in blue and purple respectively. The CAG repeat is depicted as a solid blue color block meaning that this repeat consists of uninterrupted stretch of CAG motifs. The gray bar inside the purple block corresponding to the CCG repeat indicates that the second motif of this repeat has an interruption. (Deletions and insertions in the haplotype sequence relative to the perfect, uninterrupted repeat are also shown when they are present.) Subsequent tracks depict alignments of HiFi reads to the consensus allele sequence. Any mismatches, insertions, and deletions are indicated by gray bars, vertical lines, and horizontal lines respectively.
The waterfall plot below depicts the same set of reads as the allele plot above. It depicts portions of reads spanning the repeat region without aligning them. The perfect copies of the CAG and CCG motifs are depicted in blue and purple respectively. The remaining portions of the read sequences are colored in gray.
