I have Illumina reads which I have barcoded prior to adding the Illumina adaptors. I now need to sort the raw reads into separate files before mapping. I'm using perl and have everything running smoothly if the barcode matches the raw sequence perfectly. My problem comes in when there is a mismatch or N called within the barcode sequence. Does anyone have an idea of how to efficiently code for this?
Many thanks.
Many thanks.
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