how to extract miRNA spike-in controls from smallRNAseq data

[heso]

Hi,
I'm processing single end Illumina Hiseq2000 miRNA data. I've got 5 miRNA spike-in controls in my samples. How could I extract those from the rest of my data? I would like to end up with 2 files, one with spikes and the other with my "real" reads.

I read somewhere that I should make a reference file with my spike in sequences for bowtie and then map my reads against it. How should the file look like?

Any other ideas/scripts/commands about solving the issue are of course welcome...

[dpryan]

Just make a fasta file and align against it.