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fixed minor grammar issues
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@@ -207,8 +207,8 @@ bonus score (tuned by `--junc-bonus`) if an aligned junction matches a junction
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in the annotation. Option `--junc-bed` also takes 5-column BED, including the
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in the annotation. Option `--junc-bed` also takes 5-column BED, including the
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strand field. In this case, each line indicates an oriented junction.
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strand field. In this case, each line indicates an oriented junction.
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**Note:** that `--junc-bed` is intended for long noisy RNA-seq reads only.
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**Note:** `--junc-bed` is intended for long noisy RNA-seq reads only.
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Applying the option to short RNA-seq reads increase run time with little
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Applying the option to short RNA-seq reads would increase run time with little
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improvement to junction accuracy.
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improvement to junction accuracy.
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#### <a name="long-overlap"></a>Find overlaps between long reads
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#### <a name="long-overlap"></a>Find overlaps between long reads
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