Calculating coverage from a SAM file

[AndrewRGross]

My goal is to determine the ratio of raw sequencing reads which produced one contig to sequence reads which formed a different contig.

Using the program Bowtie2, I can map unassembled reads to my contigs of interest. Once I do, I'm left with a Sequence Assembly/Map (.sam) file. I'd like to know the number of reads which map to each residue in a contig. Ultimately, I'd like to be able to say that the sequencer generated ~100x coverage of RuBisCO gene #1, ~200x coverage of RuBisCO gene #2, and ~5000x coverage of 16S genes.

Can anyone recommend a paper where this was done well or a program commonly used?

[GenoMax]

You can use BEDTools (coverageBED) or Samtools view (to get coverage) or mpileup (to get consensus), specifying the region you are interested in getting the coverage from. There are multiple threads discussing both these options on SeqAnswers.

Here is a recent thread that has references a couple of other threads with details on how to use those commands: http://seqanswers.com/forums/showthread.php?t=40928

[AndrewRGross]

Thank you very much. I apologize for posting on a subject that I am sure has been covered in other threads. For what its worth, I tried to search for other threads, but I don't think I have the right vocabulary to search for this.

Feel free to suggest search queries or threads which cover these topics. Any help is greatly appreciated.

[GenoMax]

In case you did not check back, I added a link to my previous post (that points to other links) with answers.

[AndrewRGross]

Great. I've looked through the links. They offer some context, but I think your original suggestion addresses my needs best. BEDtools coverageBed command looks like exactly what I'm looking for. SAMtools view command might also work.

Thanks again.