Comments (2)
Hi Jiahe,
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basically yes, the non-redundant library is to keep the representing piece of an element. Please read the supplementary method section, an LTR-RT is split into three pieces: LTR-IN-LTR. These pieces are pooled together among others, then the representing piece will be kept based on the 80-90-100 rule (or similar, I forgot the exact number, please find it in the paper).
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This information is indicated in the screen output and also the manual. All reliable intact LTR-RTs are listed in the genome.fa.pass.list file, including the non-TGCA LTR-RTs.
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not sure what are the five categories, but yes, non-TGCA LTR-RTs listed in both *.pass.list files are qualified intact LTR-RTs, and also included in the library.
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This information is available in the *.out.fam.size.list file. Again this information is available in the manual.
Thanks,
Shujun
from ltr_retriever.
Thank you for your answer, this will be very helpful to me.
Best,
from ltr_retriever.
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