In the lab I conjugated a bacteria of interest with E. coli and was able to transfer an antibiotic resistance gene. I do not know what this gene is. I have tried molecular approaches to determining the identity of the gene without success. I have now sequenced the conjugated E. coli with the resistance gene and have a fastq file. I am looking for advise in how to 'subtract' the E. coli sequence and leave the transferred sequence(s). I have tried lastZ, but get short reads that don't give me much information (usually below 150 bp).
Mapping the sequences to examine those that do not map (in effect, "subtracting" these out) will be difficult results to interpret (poor quality reads will also not map plus probably other reads for various reasons). But isolating and assembling those reads could be part of a solution. The Tool Shed has tools for assembly and downstream analysis, that you can compare to known methods (publications, etc).
Good luck with your project, Jen, Galaxy team