Question: Equicktandem Search Not Yielding Any Results
gravatar for Harry Podschwit
6.6 years ago by
Harry Podschwit10 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 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
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ADD COMMENTlink written 6.6 years ago by Harry Podschwit10
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