I have RNA Seq data, three replicates each and paired end (WT vs KO). I want to quantify the repetitive elements. I gone through several papers and blogs to know about Repeat Masker.
This is my command
RepeatMasker -s -nolow -species human -dir outout/dire -a -inv -lcambig -small -source -html -gff KO_1.fastq
This is the error i got it back.
RepeatMasker quit because the file KO_1.fastq only contains ambiguous bases, if any.
First of all i don't know how to supply the paired end data to the repeatmasker. Second, i could not comprehend the error. So can you please some one help me with this.