over-representation of sequences that map to "Drosophila melanogaster signal recognition particle
I found over-representation(count:114784, 1.65%, No Hit) of sequences that map to "Drosophila melanogaster signal recognition particle" but with my current knowledge, I am still unsure whether I should remove these reads from my TRAP-Seq data.
"signal recognition particle (SRP) controls the transport of secretory proteins into and across lipid bilayers"
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Why do you want to remove some sequences? Without more details on the experiment and how the data was processed, it's impossible to answer.
The data is intact, I just ran FastQC on the fastqc files. I said I was unsure not that I want to remove the sequences. I was hoping someone could explain if this is a typical artifact of Ribo-Seq data (others have posted a similar question with no answers yet). Thanks for your comment though.