Hi! I would like to check the expression of my gene of interest in expression data loaded fro SRA. It should be induced comparing activated vs non activated cells. At this stage it would be enough to visualize on the genome browser the signals of the mapped reads in the two different conditions. I have used Bowtie2 to map the reads and visualize them on the UCSC browser. It seems to work, but my questions are: 1) am I missing some steps, before the mapping? 2) do I have to run Cutadapt first? 3) do the data have to be normalized somehow in order to be able to compare the tow conditions?
Thanks a lot for the help!