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Add option to ignore -e flag in stringTie #206

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husensofteng opened this issue May 24, 2019 · 1 comment
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Add option to ignore -e flag in stringTie #206

husensofteng opened this issue May 24, 2019 · 1 comment

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@husensofteng
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The -e flag in stringTie forces it to only report transcript that are found in the reference GTF file. Skipping the -e flag below would enable performing reference-guided de novo assembly.

rnaseq/main.nf

Line 1032 in 37f260d

-e \\

I wonder if it would be possible to add a parameter to skip this flag.
@drpatelh drpatelh mentioned this issue Jun 18, 2019
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@drpatelh
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--stringTieIgnoreGTF parameter has been added in PR #195, and will be fixed when the salmon branch is merged into dev

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@husensofteng @drpatelh