LiBiNorm has an additional mode: "LiBiNorm model" for supporting extended analysis of RNA-seq data, options for producing bed and fasta files as well as additional test and development modes that can be enabled by recompiling the source with specific options enabled.
The "LiBiNorm model" mode allows a slightly more detailed exploration of global bias to be performed than is the case with "LiBiNorm model". It takes as input data a "landscape file" that can be generated by LiBiNorm which contains the locations of the reads within the transcripts. This loads more quickly than the bam and feature files so "LiBiNorm model" is more efficient if different options are being explored.
This is described in more detail.
LiBiNorm bed and refSeq
Command line format is LiBiNorm bed [options] <gff_file> and LiBiNorm refSeq [options] <gff_file> <hisat2 fileroot>
Outputs a bed format or fasta file that identifies the genomic regions associated with the transcripts to which LiBiNorm count would align the reads given the options. <gff_file> is a gtf or gff3 file identifying the genomic features and <hisat2 fileroot> is the root of a set of hisat2 index files corresponding to the associated reference genome. The output bed or fasta data can be send to a file by suffixing with > <filename>
The two options supported are
-t <feature type>, --type=<feature type>
-i <id attribute>, --idattr=<id attribute>
which perform the same roles as when used within LiBiNorm count.
The LiBiNorm code includes additional tools for comparing landscape files with each other and also for comparing landscape files with gene lists. These tools are made available by recompiling the source with #define LIBITOOLS within Options.h uncommented. More information about the tools is available.
Additional LiBiNorm count and model and options can be enabled by removing the comment marks before specific #ifdefs in the Options.h file.
These options are described in more detail.