@@ -93,12 +93,16 @@ The `PrepareDataForInteractiveBinning` function performs the following steps:
...
@@ -93,12 +93,16 @@ The `PrepareDataForInteractiveBinning` function performs the following steps:
1. Reads optional binning results from automated methods
1. Reads optional binning results from automated methods
1. Combines extracted information with sample abundance levels into the files which are expected by ICoVeR.
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
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`.
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
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.
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.