The LiBiNorm code includes some additional tools which become available if the source code is compiled after uncommenting #define LIBITOOLS in Options.h.

Comparing two landscape files

The LiBiNorm land mode allows the contents of two landscape files to be compared. The command format is:

LiBiNorm land -g <gff_file> -i <attribute> -b <bamfile> <landscapefile1> <landscapefile2>

A single file is generated that combines both landscape files, putting the entries for the same gene one after each other so that they can be compared. The gff file is used to provide coordinates for the genes/transcripts, as identified by attribute so that they can be viewed easily on IGV. The bam file allows the correct chromosome names to be used, the mapping being done based on chromosome length.

Comparing a landscape file and a gene list

The LiBiNorm land2 mode allows the contents of a landscape file to be compared with a gene list. Three output files are produced.

LiBiNorm land2 <landscapefile> <genefile>

• <filename>.subset.txt is a landscape file that contains the data for the genes/transcripts in the list.
• <filename>.unused.txt is a landscape file that contains the data for the genes/transcripts not in the list.
• <filename>.extragenes.txt is a list of the genes associated with the .unused.txt landscape file

Investigate the variation in the log likelihood with a parameter value

The LiBiNorm variation mode calculates the variation in the log likelihood value.

LiBiNorm variation [Options] -N <resultsFile> -p <parameterFile> <landscapeFile>

This calculates the log likelihood for the data in the landscape file (only using the genes that are marked as to be used for parameter finding) and saves the output in <results>_variation.txt.