Does Bowtie2 give, as output, a SORTED bam file ?
If it doens't, how could I solve this problem?
If it does, can I merge two biological replicate, e.g. ChIP ER E2 R1 and ChIP ER E2 R2, together with a tool?
In Galaxy, bowtie2 will return a sorted BAM file. If you need to merge BAM files you can use the "Merge BAM Files" tool under "NGS: SAMtools".