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Example of --frag=yes #41

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sjackman opened this issue Oct 24, 2017 · 2 comments
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Example of --frag=yes #41

sjackman opened this issue Oct 24, 2017 · 2 comments
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@sjackman
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Is -x sr --sr --frag=yes intended for paired-end short reads? Could you please give an example of its use?
@lh3 lh3 added the question label Oct 25, 2017
@lh3
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lh3 commented Oct 25, 2017

See examples here:

minimap2 -ax sr ref.fa reads-se.fq > aln.sam           # single-end alignment
minimap2 -ax sr ref.fa read1.fq read2.fq > aln.sam     # paired-end alignment
minimap2 -ax sr ref.fa reads-interleaved.fq > aln.sam  # paired-end alignment

-x sr automatically applies both --frag=yes and --sr.

@lh3 lh3 closed this as completed Oct 25, 2017
@sjackman
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Thanks for the explanation, Heng.

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@sjackman @lh3