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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Questions about whether can RepeatMasker find tandem repeats #177

Closed 1835033964 closed 1 year ago

1835033964 commented 1 year ago

I noticed that when I install the RepeatMasker, the path of trf is needed. I would like to know whether it is means RepeatMasker can help me to find tandem repeats and I don't have to run trf to find them again ? Thank you!

rmhubley commented 1 year ago

RepeatMasker is primarily concerned with locating TEs, however we do also use TRF to identify simple/tandem repeats to mitigate false positive matches to TE families that contain simple/tandem segments. We also employ TRF to label the unmasked sequence after all TEs are identified. Please note that we do restrict TRF to period sizes <= 10 for our purposes as we prefer to use satellites defined in our libraries for annotating longer tandem stretches, although this may change in future releases as we plan to change the way alignment evidence is adjudicated.