Will bowtie multi-valid-alignment-report confuse downstream software?

Question

[--panda--]

I'm wondering what will happen if we choose the option that makes 'bowtie' report multiple valid alignment to the sam file. Will the downstream software(if you think it's not specific, take 'cufflinks' as the software used here) get confused about which alignment to use?

Answer 1

[WouterDeCoster]

Multimapping reads will be flagged in the sam/bam file and for any downstream analysis for which this might be a problem, the software will take that into account. E.g. read counting generally ignores all multimapping reads.

[--panda--]

That sounds reasonable. Thanks.