All reads are in the SAM file; you can filter to remove unmapped reads as needed.

J.

On Nov 7, 2013, at 5:36 AM, Benjamin Osei-agyeman <benjy_osei@yahoo.co.uk> wrote:

Hi

What are the contents of a SAM file after Bowtie has been run? Does it contain all reads or only those reads mapped to the genome?

Thanks

Benjy
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