I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from WormBase. I have installed nhmmer using conda.
I have then run the following command:
repeatmasker -s -lib RepBase23.08.fasta/celrep.ref -dir annotation/ -gff c_elegans.PRJNA13758.WS266.genomic.fa
I then imported the annotation table into R. I notice that some transposons have a length of 1!
How is this possible?!
Also, how can repeatmasker calculate such percent divergence, deletion, insertion with a query width of 1? For some of these predictions, both the query and repeat lengths are 1 (so an alignment of 1 nucleotide against 1 nucleotide!)! But the Smith-Waterman scores don't match this. There is something important I am missing here. Can someone help me interpret the table below and explain why some transposons have a length of 1 in the genome?