I have a transcriptome based on our Pacbio Iso-seq data. I use the transcriptome as input to RepeatModeler and then get the consensi.fa.classified file and IsoseqDB-families.fa. Next, I run Repeatmasker to annotate my transcriptome. How do I interpret the results? I have many sequences which are labeled "unknown". Are they the de novo transposable elements? I also want to obtain the loci of the de novo transposable elements from the control and treated transcriptome then I can check if the treated sample has more newly inserted transposable elements. Do you know how to get the loci of the de novo transposable elements? Many thanks in advance for any suggestions and replies!
Hi, thanks for developing this powerful software!
I have a transcriptome based on our Pacbio Iso-seq data. I use the transcriptome as input to RepeatModeler and then get the consensi.fa.classified file and IsoseqDB-families.fa. Next, I run Repeatmasker to annotate my transcriptome. How do I interpret the results? I have many sequences which are labeled "unknown". Are they the de novo transposable elements? I also want to obtain the loci of the de novo transposable elements from the control and treated transcriptome then I can check if the treated sample has more newly inserted transposable elements. Do you know how to get the loci of the de novo transposable elements? Many thanks in advance for any suggestions and replies!
Best, Dongxu Zheng