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Old 09-29-2014, 04:28 AM   #1
Location: Sweden

Join Date: May 2014
Posts: 19
Question how to extract miRNA spike-in controls from smallRNAseq data

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...
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Old 09-29-2014, 04:48 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Just make a fasta file and align against it.
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