Hi all,
I used progressiveMAUVE to align 4 bacterial genomes (~4Mb each), which ran
with no error. I need to now parse the text sequences to pull specific
positions from each (using the first sequence as a reference for position
number) for use as outgroups in a SNP tree. However, I've noticed a
seeming inconsistency in what I see in the GUI representation of my
alignment file versus what I see in the text file. More specifically, the
text file indicates that there should be gaps (very long gaps in some
cases) at certain positions in the first sequence, but when I look at the
corresponding position in the GUI browser, I don't see any gaps at those
positions in the first sequence, and indeed see far fewer gaps in the GUI
than what is represented in the text file. As I need to pull thousands of
specific SNP positions, I'm not quite sure how to deal with this seeming
inconsistency.
Is there something fundamental I'm missing here? Hopefully this question is
clear.
Thanks in advance for any possible help!
Carmela C
SDSU Biological and Medical Informatics Research Center
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