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The input parameters that we typically use with color space data are the following:
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gmapper-cs -p opp-in -N 4 -1 F3/V3BC17_RNA.csfasta -2 F5/V3BC17_RNA.csfasta /home/scott/Downloads/mouse.rna.fna > bc17.sam 2> bc17.log &
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Tip: To view the actual alignments in base space as part of the output file, add -p option (prettyprint).