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how to extract miRNA spike-in controls from smallRNAseq data

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  • how to extract miRNA spike-in controls from smallRNAseq data

    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...

  • #2
    Just make a fasta file and align against it.

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