Question: Why do I see 3-nucleotide periodicity in RNA-Seq?
gravatar for Apex92
13 days ago by
Apex9220 wrote:

Hi everyone. I have a question regarding one of my plots that I made out of a bam file. We have performed the RNA-Seq and after thebowtie alignment, I tried to plot the frequency of each leftmost (4th column in bam file) nucleotide position for the mapped reads. In this way, I tried to figure out how many reads mapped to each nucleotide position on mRNA.

After I got the plot, I noticed that after a specific position (e.g. 160) the frequency of mapped reads drops in my plot, meaning that in each third nucleotide position I see a very low amount of reads (4-5) mapped. Even though we have not performed a Ribo-Seq could you experts share your ideas why do I see such a drop of mapped reads in my plot? Can it be because of the ribosome movement on mRNA?

I have included a representation of my plot as well.

Many thanks.

ADD COMMENTlink modified 13 days ago • written 13 days ago by Apex9220

I have no answer but are you aware that bowtie is not splice-aware?

ADD REPLYlink written 13 days ago by ATpoint40k
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