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Old 08-17-2017, 05:35 AM   #2
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Unless it is explicitly stated that a reported DNA sequence is presented in a 3' to 5' orientation it is accepted convention that all DNA sequences are written 5' to 3'. All sequence data reported by an Illumina (or other) sequencer is in 5'->3' orientation. BLAST or any other sequence alignment program expects and assumes that your input FastQ files are 5'->3'. These programs all internally manage the alignment of the query to the reference in both the its input orientation and its reverse complement.
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