Question: Visualizing BowTie2 BAM File?
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mkpelletier • 20 wrote:
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.
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modified 3.5 years ago
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Philipe Moncuquet • 40
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4.6 years ago by
mkpelletier • 20
You have mentioned "zooming". Are you already using some genome viewer, like Trackster, UCSC or IGV? In all of them you should be able to see the base pairs. You can use all of them from Galaxy.
It says "trackster" under visualization "type" when I look at the saved visualization. I see a bunch of grey bars that are aligned to the reference genome with positions, but can't see any nucleotides.
Here is a screenshot...http://mkpelletier.imgur.com/all/
It says: "mkpelletier's images are not publicly available."
try http://i.imgur.com/qGcahAo.png
http://i.imgur.com/qGcahAo.png is another link that might work if the first one is presenting difficulties.