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PacificBiosciences / trgt

Tandem repeat genotyping and visualization from PacBio HiFi data
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question regarding understanding trvz plot #24

Open Tianyibian opened 9 months ago

Tianyibian commented 9 months ago

Hi, when looking at the gene HOXD13, and many other genes containing a similar motif pattern containing an unspecific base pair N, I used trvz to plot these genes and realized that the resulting trvz plot have quite a lot of grey areas image. I propose that these grey areas are not true mismatches but representing the N base pairs. Am I guessing it correctly? If so, would it be possible to have improvements in the future so these grey areas will be removed, or is there any other specific meanings that these grey areas are representing that I missed? Thank you so much for your response if you could.

egor-dolzhenko commented 9 months ago

Thanks for catching this! We are planning to implement support for IUPAC codes in TRGT and TRVZ soon. When this is done, the N bases will no longer appear as mismatches in TRVZ plots. Tentatively, we are planning to implement this in v0.9.0.