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?


Transposons of length 1

  • $\begingroup$ The image only contains transposons with a width of 1 as far as I understand. I've selected the rows where queryBegin == queryEnd. The queryBegin variable = queryEnd for all the lines here. It is a subset of the original data frame. $\endgroup$ – charlesdarwin Nov 6 '18 at 17:42

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