RepeatMasker error
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.
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mark.ziemann
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PK •
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can RepeatMasker read fastq file (?)
This is the SYNOPSIS of Repeat masker. Am i wrong?
... yeah .... fasta , ..... not fastq
Okay Great Thanks, Do you think other parameters are fine?
Also I have one more question. How do i supply paired end data.
with ... "paired-end data"... that only means FASTQ... what are you exactly trying to do with repeatmasker ?...
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
Just use the first read in the pair. I've done this before and it works just fine.
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.
That's right, RepeatMasker will give you the % sequences that match each class of repeats. If there are differences, they should be obvious.