RepeatMasker error

Question

[PK]

Hi all,

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.

[Pierre Lindenbaum]

KO_1.fastq

can RepeatMasker read fastq file (?)

[PK]

  RepeatMasker [-options] <seqfiles(s) in fasta format>

This is the SYNOPSIS of Repeat masker. Am i wrong?

[Pierre Lindenbaum]

... yeah .... fasta , ..... not fastq

[PK]

Okay Great Thanks, Do you think other parameters are fine?

[Pierre Lindenbaum]

 ¯\_(ツ)_/¯

[PK]

Also I have one more question. How do i supply paired end data.

[Pierre Lindenbaum]

with ... "paired-end data"... that only means FASTQ... what are you exactly trying to do with repeatmasker ?...

[PK]

My hypothesis is that my protein of interest is binding to Repetitive elements. So, I knock out the protein and prepared the library. So I have three replicates of WT and KO. I want to quantify is there any difference between WT and KO samples. Do you understand? If not please ask me. I can explain

[mark.ziemann]

Just use the first read in the pair. I've done this before and it works just fine.

[PK]

Oh Okay, Thanks. My idea is get it done Repeat Masker for WT vs KO and directly compare to find the difference. or What else would you suggest to find the difference.

[mark.ziemann]

That's right, RepeatMasker will give you the % sequences that match each class of repeats. If there are differences, they should be obvious.