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README.md
@@ -37,7 +37,7 @@ For paired-end data you can run Read1 and Read2 in parallel and then concatenate
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# Paired-end mode
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-For certain downstream applications, you may want to retain proper paired-ends.
+For certain downstream applications you may want to retain proper paired-ends. The paired-end mode of the filter subcommand is:
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`rdxon filter -x kmer.x.map -y kmer.y.map -o <outprefix> <read1.fq.gz> <read2.fq.gz>`
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