GenomeComb
cg multicount ?options? multicountfile countfile countfile ?countfile? ...
Compare multiple count files that all have the same ids (depricated)
This command combines multiple count (or other) files into one multicount file: a tab separated file containing a wide table used to compare genes/exon/.. (counts) between different samples. Each line in the table contains gene/exon/.. names and columns with the count 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_weighed-isoquant-sample1.tsv.
The command matches rows in the different files based on having the same id, i.e. the combination of values in one or more id fields. The fields potentially used for this can be given using the -idfields option (defaults to any of the following: geneid, genename, gene, exon, exonid, id, name, cell, cellbarcode, spliceName, chromosome, strand, start, begin, end). Only the fields present in all files will actually be used (so you have to make sure at least one value that is unique to each row is present)
If there are fields with a - in them, these will be use as data fields. If not, all fields not in "idfields" will be considered data fields, and the columns will be named <field>-<sample> where the <sample> part is extracted from the file name. When there is no with a certain id one (or more) of the files, it's data fields will be filled with 0 (by default)
Variants