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. https://ibb.co/G51pDLm
Many thanks.
I have no answer but are you aware that bowtie is not splice-aware?