Bowtie2 - how many output sam files?

[sells78]

Hi all,

My query is 'should bowtie 2 produce a separate SAM file for each pair of input reads from different samples?'

When specifying -1 and -2 and comma separated lists of input file for read 1 and 2, which are in the correct order and represent reads from different individuals - shouldn't a sam file be produced for each individual sample alignment?

Many thanks


J

[dpryan]

No, it should only produce one SAM file. The "comma-separated list of input files" syntax is only used for technical replicates that should be merged into a single file.