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PacificBiosciences / trgt

Tandem repeat genotyping and visualization from PacBio HiFi data
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Short read data compatibility #11

Open JannahS opened 1 year ago

JannahS commented 1 year ago

Hi there,

Can I use trgt to call repeat expansions from short read data (illlumina data for example) ? If yes, is there any caveat?

Thanks in advance.

egor-dolzhenko commented 1 year ago

Thank you for the question! TRGT is designed for long-read HiFi data and won't work with short reads. However, there are many other tools made specifically for analysis of repeats in short-read data that you could try.

hdashnow commented 1 year ago

Depending on your specific variant types/project goals, a few tools you might look at are, in no particular order: GangSTR, STRling, HipSTR, ExpansionHunter, ExpansionHunter Denovo

atimmaraju commented 9 months ago

Hello,

Is TRGT compatible with amplicons (~200bp) sequenced on pacbio, with the hifi reads aligned with BWA?

Thanks, Arun

egor-dolzhenko commented 9 months ago

Hi Arun,

Thanks for reaching out. Would you be open to sharing some details of your assay? This would help us to provide concrete suggesitons. Please feel free to reach out by email.

Best wishes, Egor