(vg rna) some transcripts have multiple projections on haplotypes and abnormal length growth

Question

[Wenhai]

When I used vg rna, I found that some reference transcripts had multiple projections on the same haplotype, and the transcript length would increase abnormally compared with the reference transcript. What is the reason for this? This seems to lead to errors in rpvg inference, because I found it by backtracking the error reports of rpvg.

Here are some examples

Name    Length  Transcripts Haplotypes
OsMH_01T0147400.1_R1        2507        OsMH_01T0147400.1        MHChr01,ZHChr01
OsMH_01T0147400.1_H1        7588        OsMH_01T0147400.1        ZHChr01
OsMH_01T0147400.1_H2        2507        OsMH_01T0147400.1        ZSChr01
OsMH_01T0147400.2_R1        1504        OsMH_01T0147400.2        MHChr01,ZHChr01
OsMH_01T0147400.3_R1        2244        OsMH_01T0147400.3        MHChr01,ZHChr01
OsMH_01T0147400.3_H1        7325        OsMH_01T0147400.3        ZHChr01
OsMH_01T0147400.3_H2        2244        OsMH_01T0147400.3        ZSChr01
OsMH_01T0147400.4_R1        1248        OsMH_01T0147400.4        MHChr01,ZHChr01
OsMH_01T0147400.4_H1        1248        OsMH_01T0147400.4        ZSChr01


OsMH_01T0285100.1_R1        1249        OsMH_01T0285100.1        MHChr01
OsMH_01T0285100.1_H1        1249        OsMH_01T0285100.1        ZHChr01
OsMH_01T0285100.1_H2        75526        OsMH_01T0285100.1        ZHChr01
OsMH_01T0285100.1_H3        171674        OsMH_01T0285100.1        ZHChr01

Thanks for your help.