Bowtie 2 outputs alignments in SAM format, enabling interoperation with a large Make sure you're getting the source package; the file downloaded should end in -source.zip . As of version 2.3.5 bowtie2 now supports aligning SRA reads.
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7 May 2013 http://www.ncbi.nlm.nih.gov/sra. I downloaded the sra file from there, next question would be : how to convert it to sam or bam file? It looks like
