Commit 0758a8bf authored by Bertjan Broeksema's avatar Bertjan Broeksema

Add note about generating penta nucleotide frequencies

parent bf7470fc
......@@ -93,12 +93,16 @@ The `PrepareDataForInteractiveBinning` function performs the following steps:
1. Reads optional binning results from automated methods
1. Combines extracted information with sample abundance levels into the files which are expected by ICoVeR.
**NOTE:** The ids in the fasta file must match the names in the abundance file.
**NOTE 1:** The ids in the fasta file must match the names in the abundance file.
Thus, if a contig in the fasta file starts with a line `>contig_123`, there must
be a line in the abundance file as where the name column has value `contig_123`.
Some error checking is done, but you should not rely on this and make sure that
the fasta file and the abundance file are prepared properly.
**NOTE 2:** Although we got good results with tetra nucleotide frequencies, it is
also possible to generate penta nucleotide frequencies. To this end you have to
change the [PrepareDataForInteractiveBinning](https://github.com/bbroeksema/ICoVeR/blob/master/R.preprocessing/PrepareDataForInteractiveBinning.R#L28) script.
Start R studio and type the following commands.
{% highlight r %}
......
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