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Have you checked to see if your data has rRNA contamination? What is
filteredin name referring to?How to check if the data has rRNA contamination?
Filters: Cut 15 nucleotides from 5’ and 3' of every read. Filter out all the reads shorter than 50. Drop the read if the average quality is below the 15
Map your reads against rDNA sequence for your organism or use a package like
sortmeRNA(LINK).Why do you think it is mRNA?
My bad. I hastily assumed it was
RNAseqthough going back to thread I don't see you saying that specifically.What kind of data is this? There can be different explanations (e.g. presence of rRNA reads is one in case of RNAseq) based on type of data you have at hand.
The data is from CHIP-seq experiment
It is possible that your experiment is enriching fragments with slightly different GC distributions. Have you tried to analyze the data? Perhaps there is nothing wrong with it.