Making the assumption that your data is DNA (and not RNA), the tools
under "NGS: SAM Tools" and "Operate on Genomic Intervals" can generate
coordinates of the mapped reads which then can be correlated with
genes/ORFs from your bacterial genome (or related genomes, if you can
obtain those those mapped to the same reference genome to use as
General analysis path:
Starting with your SAM file, use these tools first to obtain an
file representing your read coverage:
1 - SAM-to-BAM
2 - Generate pileup
3 - Pileup-to-Interval
Next, import a reference known gene set. Sources may include UCSC,
or other. Download from that source (if not directly available via a
"Get Data" source) and upload the file into Galaxy using FTP ("Get
-> Upload"). If this data is in GTF/T format, you can convert it to
Interval using "Convert Formats -> GFF-to-BED" (BED is a stricter form
of Interval, use the pencil icon in the datasets box to Edit
to change data type to Interval).
Then if using output from "Pileup-to-Interval" and a reference known
gene/transcript dataset mapped to the same reference genome, use the
tools in "Operate on Genomic Intervals" to perform comparisons based
genomic coordinates. Each tool has a description on the main tool
but there are also screencasts explaining the functions here under "3.
Interval Operation Tutorial"
Also see: "Regional Variation -> Feature coverage" for localized
Once an intersection of coordinates is complete, you may need to use
tools in "Text Manipulation", "Filter and Sort", or "Join, Subtract
Group" to merge in gene identifiers. Exactly what order to use these
tools greatly depends on the input reference gene/transcript dataset
If you are doing transcript predictions, the tool "EMBOSS -> getorf"
Finds and extracts open reading frames (ORFs)" may be helpful. This
requires sequence as input. Once predicted transcript coordinates are
obtained, extract sequence from the reference genome using "Fetch
Sequences -> Extract Genomic DNA" to use as input.
Hopefully this helps to get you started. Please let us know if we can