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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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LTR_retriever produce different result in different data combine ways #172

Open LQ16 opened 4 weeks ago

LQ16 commented 4 weeks ago

Hi @oushujun, I apologize for the inconvenience, but I'm facing an issue that I don't understand. When I run LTR_retriever using two different methods, I get different results. In the first method, I use:

LTR_retriever -genome $fa -noanno -inharvest 1.fa.mod.harvest.combine.scn -infinder 1.fa.mod.finder.combine.scn -threads 20

In the second method, I combine the input files first:

cat 1.fa.mod.harvest.combine.scn 1.fa.mod.finder.combine.scn > all.scn LTR_retriever -genome $fa -noanno -inharvest all.scn -threads 20

I noticed that the second method produces more LTR counts than the first method. Which result should I adopt?