getting gene sequences from ion xpress

Question

[Astoulpho]

This is probably a beginners question, but since I have been struggling with it for some days now, I am trying to find some help here. We have to get a gene's sequence for some individuals, these genes were sequenced using ionxpress and I got the fastq and bam files.The question is, how do I get the gene's sequence for each individual?

thanks for the help

ps. I am using galaxy and it is human gene

[igor]

Is this DNA or RNA sequencing? Do you need to get the official gene sequence or do you expect your samples to have some differences from the known sequence? If you are looking for differences, then what you are looking for is variant calling or detection.