Good Morning: I am new to Galaxy, and have a question about the BowTie 2 BAM file. I had BowTie2 align my Arabidopsis thaliana reads to the TAIR v10 database, and that seems to have gone well, as I can see most of the reads have aligned just fine. What I cannot figure out is how to visualize the actual sequences of the reads (GATC, etc) relative to the reference genome. Is there a simple way to do this? Simply zooming in does not seem to do the trick. Thanks in advance.
Trackster, the Galaxy Genome viewer, is able to show also the nucletide sequences. You only need to zoom in. Zooming can be done either vie the (+) (-) Zooming buttons on top, or you can select a region of interest. If that region is small enough you will see the nucleotides.
I am having the same problem here. I work on the hg19 build with some reads fro chr20 and no matter how deep I zoom in I can't see nucleotides sequence as per the example shown by Bjoern. I have check that the build is well recognised, when I had a vcf file track with variant I am actually able to see this nucleotide but not for the reference.