Problems visualizing Mosaik alignment with Gambit

[josecolquitt]

I have been working with short reads in Mosaik. I have developed an aligniment using the program and used the mosaikAssembler program to creat a BAM file for analysis in Gambit. Gambit asks for the BAM file for the actual alignment, and the original reference genome in FASTA format. I selected both and selected the "use existing index" for both the BAM file and the FASTA file (perhaps this is the issue..)?

Once I save the session and try to open up the visualization, nothing is displayed. If anyone has any insight on this it would be greatly appreciated as I'm very new with this and my internship mentor doesn't have any solutions either.

[josecolquitt]

Alternatively, a few suggestions on other methods to accomplish this task would be appreciated as well:

I am trying to align a 4 fasta short read files to there original genome. We just need to be able to align these files to the genome and analyze each of the 4 alignments separately (to look at polymorphism etc). The programs that I have tried thus far have been a challenge due to my lack knowledge of the ins and outs of the applications.

I would appreciate any input that would aid in this issue, as these are my first dealings with these types of applications.