Question: Equicktandem Search Not Yielding Any Results
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Harry Podschwit • 10 wrote:
Hello all,
I am certainly new to using galaxy and I have already checked the
message boards to get some assistance on this but was unsuccessful.
Anyways, here is my problem, I have a a FASTA file of C. gigas partial
sequences. I was trying to use Galaxy's equicktandem tool to identify
micro satellites in the sequence. However, when I ran the tool it did
not yield any results. This is strange because I could visually pick
out where l thought the algorithm should have found a hit.
Additionally, trimming my collection of sequences to a single sequence
did not yield any hits. Moreover, I created a fake sequence with very
obvious "microsatellites" and the algorithm appeared to work fine as
it identified the repeats. While I suppose it is certainly possible
that there may just not be any microsatellites in my sequence, I find
it highly unlikely and suspect something else is going on. This seemed
like such a simple tool yet I am having much difficulty in using it. I
am simply uploading my FASTA file normally and then taking that file
and using the tool. I am doing this all online through the galaxy
website not a local instance and if you would like to see yourself the
FASTA file can be downloaded at
http://genefish.wikispaces.com/crassostreome and the FASTA file is
cgigas_alpha_v0.3.2 (the collection of 272 sequences). Please help
this has been excruciatingly frustrating for me and I suspect that a
veteran Galaxy user may be able to see my error quickly.
Best,
Harry
hpodschwit@gmail.com