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JinfengChen / RelocaTE2

RelocaTE2
MIT License
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Can RelocaTE2 be used without RepeatMasker output file ? #16

Open cecilelorrain opened 5 years ago

cecilelorrain commented 5 years ago

Hi,

I would like to use RelocaTE2 on population data that I have. But in a previous work I have annotated the TEs oin the reference genome using REPET (https://urgi.versailles.inra.fr/Tools/REPET) and not RepeatMasker. Can I replace the "-r REFERENCE_INS" by a .bed file with positions of annotated TEs?

Thank you in advance for your answer, CecileLorrain

JinfengChen commented 4 years ago

Hi Cecile,

RelocaTE2 uses RepeatMasker output because it has information on whether the annotated regions contain TE ends. This is critical for identifying nonreference insertions and removing false-positive calls. RelocaTE2 will create a bed file from RepeatMasker output. Using user-specified bed files may result in great loss of accuracy. You can run RepeatMasker with repeat library generated by REPET and use *.out file in RelocaTE2. Thanks.

Jinfeng