I've got paired-end MiSeq RNA data from Illumina, with as far as I know adapters/primers/barcodes clipped off. When mapping this data with bowtie2 against the human reference mRNA's I don't find even 1 global alignment in +- 500 sequence pairs.
Could this be due to the UTR's probably still in the sequences and not in the references? Or doesn't that matter for global alignment?
Could this be due to the UTR's probably still in the sequences and not in the references? Or doesn't that matter for global alignment?
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