Dear all,
I am very new in the TE field. I have run RepeatModeler on a newly assembled genome and as a result got the following files: families.stk and consensi.fa.
As I understand, consensi.fa file has all the repeats predicted and I can create consensi.fa.classified by running RepeatClassifier. But I still do not understand what to do with these files in order to see the content and variety of the repeats "my" genome has. I did not find any clear explanation on that in the RMasker or RModeler github pages. What would be the basic, general command to get the info I need?
Note: I am not interested in masking my genome. I need to understand its TE and repeat content.
Thank you!
OK, I kinda got it. I ran
RepeatClassifier -consensi consensi.fa
and then
RepeatMasker -pa 4 -q -dir . -small -gff -lib consensi.fa.classified assembly.fasta
But another question now:
Where can I find examples of the content of repetitive elements for human, for example? I am looking at one of the output files - assembly.fasta.tbl - where all the repetitive elements found are listed. I would like to compare it with some other genome to have an understanding of what I am dealing with :)
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