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  • rRNA & tRNA contamination in whole genome sequencing

    Hi folks

    I had a peculiar phenomenon happening with my genome reqsequencing project and was wondering if other people have seen this.

    I've been using Qiagen's DNeasy kit to isolate Drosophila DNA and submitted for whole genome sequencing on a Illumina Hiseq2500 platform (Truseq for library prep).

    This is a reference based genome resequencing project and I've been reassembling some of the bacteria genome that lives inside the fly and what was strange with my alignment was that I was getting alot of false alignments only around the rRNA and tRNA genes. The coverage doubles around the rRNA and tRNA genes and the only explanation I had was the secondary structure or the sheer massive amounts of those nulceotides had survived the RNase treatment.

    Have people seen this before? And are there recommended protocols to decrease the amount of rRNA and tRNA in your DNA sample?

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