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Update salmon_tutorial.rst
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halexand committed Oct 12, 2016
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Expand Up @@ -36,7 +36,7 @@ Grab the nucleotide (``*ffn``) predicted protein regions from Prokka and link th

Create the salmon index:
::
salmon index -t metag_10112016.ffn -i transcript_index --type quasi -k 31
salmon index -t metag_10122016.ffn -i transcript_index --type quasi -k 31

Salmon requires that paired reads be separated into two files. We can split the reads using the ``split-paired-reads.py`` from the ``khmer`` package:
::
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