Does bowtie randomly select a match from two equally valid alignments?

[Kennels]

Hello

I've read the bowtie manual but am still not very clear.

I have some sRNA NGS data, and want to align using bowtie to a hairpin reference (sense and antisense sequence of a gene in one fasta file).

I would expect that a read from the hairpin would align equally well to both the sense and antisense sequence.

In this case, does bowtie randomly select the alignment to report?

Should I be aligning only to the sense or antisense sequence using the --norc or --nofw options?

Also, can anyone clarify what this means about the --best option for bowtie:

"--best mode also removes all strand bias"

Thanks for any advice!

kennels

[Kennels]

At the start of the manual its says:

##########
In the default mode, bowtie can exhibit strand bias. Strand bias occurs when input reference and reads are such that (a) some reads align equally well to sites on the forward and reverse strands of the reference, and (b) the number of such sites on one strand is different from the number on the other strand. When this happens for a given read, bowtie effectively chooses one strand or the other with 50% probability, then reports a randomly-selected alignment for that read from among the sites on the selected strand. This tends to overassign alignments to the sites on the strand with fewer sites and underassign to sites on the strand with more sites. The effect is mitigated, though it may not be eliminated, when reads are longer or when paired-end reads are used. Running Bowtie in --best mode eliminates strand bias by forcing Bowtie to select one strand or the other with a probability that is proportional to the number of best sites on the strand.

###########

So a more specific question is, what if there are equal number of sites on both sense and antisense?