This might be old. I wonder some bowtie guru can explain that what defines a valid alignment, and what defines a reportable alignment. Some people recommend '-m 1' for uniqueness, others suggest to do '-k 2' and filtering the reads with multiple alignments in the MAP/SAM file. Surely there are differences. Which one is better for ChIP-seq?
![Confused](https://www.seqanswers.com/core/images/smilies/confused.png)