about trgt plot on complex tr

[WeiCSong]

Hi,
I ran trgt on version 1.0 trgt annotation #37 (comment)_ and one of the complex TR:

chr19 53958673 53959528 ID=chr19_53958673_53959528;MOTIFS=CCCCACCCCTC,CCAGGTACCTTCTACCAT,CA,TC,CCTCCCCCAATTTCTC,TCTCCCTCCC,CCCT,CCCTCCCCCTCCCT,TCTCTCCCTC,GTCCCT,CT,TCTCTCTCTGGATA,TG,TC,TCTCTGGTCTC;STRUC=GGGCTTCCTTCGGGTGCATCCCCAG(CCCCACCCCTC)n(CCAGGTACCTTCTACCAT)n(CA)n(TC)n(CCTCCCCCAATTTCTC)n(TCTCCCTCCC)n(CCCT)n(CCCTCCCCCTCCCT)n(TCTCTCCCTC)n(GTCCCT)n(CT)n(TCTCTCTCTGGATA)n(TG)n(TC)n(TCTCTGGTCTC)nCAGCTCCGCACTTTACCCAGCGACA

is quite confusing in trgt plot. Below is the genotype:

4_4_5_3_3_12_3_0_18_4_39_4_0_0_10,4_4_8_5_3_3_0_7_18_4_40_4_0_0_10

and below is the plot:

It is not easy to match each TR count to the motif in the plot by bare eyes, and it seems that the order is not the same as the STRUC in the annotaion (the first and second motif on the left did not repeat four times?). I also retrieved hg38 reference sequence of this region:

chr19:53958673-53959528
TGGGCTTCCTTCGGGTGCATCCCCAGTCTCTGTGTCTGCCTCTGTTTCTCTGGATCTCTC
TCTCTTCCTGTCTCAGTCCCTCTCCGTCTGTCTCTCTCTGGGTCTCCCTCTTTTCCTGCA
CTTGCCTTTCTTTCCCCAGGTACCTTCTGCCATCCAGGCCCTTCTACCCTCCATTTCTTT
CATTTACTATCTTGCTCCCCCGCTCCCTCTCCGCATCTTCTTCTCTCTTTAAAGCTTCCT
TCTCTCTAGCAAGACCTTGCCCCCATCCCCAATTTCTCTCCCTACCCGCTCTCCATTTCA
TTCCCTCTCCCCCCTCTCTCCCCCATCCTCTCAGTCTCTCTCTTTCTGTCTGTCTCTCCC
CATCTGTCCCTCCTCCCTCCTCTCTGGATGACTCTCTCCCTCTCTCTTCTTTCCTTCTGT
TTCCCAGATCCTGACCCCCCCCACACACACACTTACCCCAGCCCTCCCCCACCCCCTCCC
CCCCAGCCCCTGCGTTTCTCTCTTTGAGTCTCTGTCCCTGTCCCCTTCTCTCTCTGGATA
TTTCTCTGTGTGTATCTCTCCAACTTCCTTCTGCTTCCAGCCGCTGCCTCCCCCAAATTT
CTCCCTCCCCCATTTCTGTTTCGCGGTCTCTGGGTCTCTCTCTTTCCGTTTCTCCTCGTC
TCTCTCTGTCTCTCTCCCTCCCTCTCTGGATCTCTCTCTTCTCCTCCGGCTTCCTTCTGC
CACTCGACCCTGCCCCCCTCTTTCCCTTCCCCCATCCATCTCCTCTCCGAGGCTCCCCAT
CCCTCAGCAGCTCCCCTCCCCCTCCCTCCCTACTCCCTCCCTCTCGTCCTCCAGCTCCGC
ACTTTACCCAGCGACA

and it was also not easy to match each motif and its order to the reference sequence. Not sure if my interpretation of the plot is wrong, or my sequence data is problematic. Hope to learn from you!

I also have two suggestion on the trgt plot function:

1. is it possible to plot reference TR on the bottom for better comparison?
2. the color legend seems broken since there are too many motifs, and some of them are out of the range. Can they be showed in multiple rows?

[egor-dolzhenko]

Thank you for the detailed feedback @WeiCSong! I agree that current TRGT plots can be confusing for very complex repeats like this. We are working on a better support for complex repeats and hopefully will have something closer to the end of the year. Can we send you some prototype plots for feedback? Also, we are about to deprecate the STRUC field (the latest versions of TRGT will report a segmentation that doesn't follow the order of motifs specified in the STRUC field if they find it).

[WeiCSong]

Thank you for the detailed feedback @WeiCSong! I agree that current TRGT plots can be confusing for very complex repeats like this. We are working on a better support for complex repeats and hopefully will have something closer to the end of the year. Can we send you some prototype plots for feedback? Also, we are about to deprecate the STRUC field (the latest versions of TRGT will report a segmentation that doesn't follow the order of motifs specified in the STRUC field if they find it).

Great @egor-dolzhenko ! Please send me at [email protected]

[egor-dolzhenko]

Thanks, will do!