GenomeComb
cg multigene ?options? multigenefile genefile genefile ?genefile? ...
Compare multiple gene files
This command combines multiple gene files into one multigene file; a tab separated file containing a wide table used to compare gene (counts) between different samples. Each line in the table contains general gene info (chromosome, begin, end, strand, ?gene?, ?geneid?) and columns with gene info specific to each sample (count, etc.). The latter have a column heading of the form field-<sample>.
<sample> can be simply the samplename, but may also include information about e.g. the sequencing or analysis method in the form method-samplename, e.g. count-isoquant-sample1.
When a gene was not detected in a sample, the value in the table is set to 0.0.
By default multigene will match based on the gene name (or geneid), For novel samples (identified based on the presence of a pattern in the gene name, default containing "novel") approximate matching is used: Novel genes will be matched if they overlap. The resulting gene will have the lowest start and highest end position of these matches. The id of these result genes will be changed to one unique for that gene and consistent over different experiments (based on location and strand)
RNA