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Update mop_preprocess.rst
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lucacozzuto authored Mar 28, 2024
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Expand Up @@ -126,7 +126,7 @@ The command line options for each tool used in the pipeline are stored within sp

.. literalinclude:: ../mop_preprocess/tool_opts/drna_tool_seqtagger_opt.tsv

The first column indicates the processing step as **basecalling** or **demultiplexing** etc. Some tools such as Guppy can be used for more processing steps.
The first column indicates the processing step as **basecalling** or **demultiplexing** etc. Some tools such as Guppy can be used for more processing steps. Several pre-compiled tool_opts files are stored within the folder **tool_opts**.

.. note::
Readucks is run after guppy demultiplexing. It refines the demultiplexing generating different fastqs
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