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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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should we only keep the pseudochromosome for caculating the LAI? #114

Closed wbglizhizhong closed 2 years ago

wbglizhizhong commented 2 years ago

Hi, shujun, Here I have a question about the calculation of LAI. After I calculated the LAI for the genome, the fragments showed 0 for LAI, should we remove these sequences for estimating the global LAI?

Best, Georgelee

oushujun commented 2 years ago

Hello Georgelee,

This depends on what you call a genome and what you want to measure. If all sequences coming out of assembly is everythhing you think is a genome, and the purpose is to measure the global LAI of the assembly, then you should include those short contigs. But if you think the short ones are not a good representation of the genome, then you should remove them from all downstream analyses (in general).

You may do either and clearly report what you did on your manuscript. i.e., "we measured the overall LAI of all pseduochromosomes/all sequnces assembled..."

Best, Shujun

wbglizhizhong commented 2 years ago

Hi shujun, Thanks for your answer.

Best, Georgelee