PRO format

The PRO (Simulation Profile) format is designed to describe the characteristics of each transcript (i.e., line) from the reference annotation, initially and after each step of the simulation (i.e., columns). Columns are tab-separated and describe the attributes:

~Column Number	Name	Value	Description
1	LOCUS_ID	chrom:start-end[W|C]	identifier for the intrinsic splicing locus, given by the chromosome (chrom), start and end position and the strand (Watson or Crick).
2	TRANSCRIPT_ID	String	transcript identifier from the reference annotation.
3	CODING	[CDS|NC]	specifies whether the transcript has an annotated CDS or not (NC)
4	LENGTH	Integer	the spliced length of the transcript molecule as annotated in the reference annotation
5	RFREQ_EXP	Float	relative frequency of RNA copies of this transcript after simulated expression
6	AFREQ_EXP	Integer	absolute number of expressed RNA molecules
7	RFREQ_LIB	Float	relative frequency of cDNA molecules derived from this transcript after library construction
8	AFREQ_LIB	Integer	absolute number of cDNA molecules generated from this transcript
9	RFREQ_SEQ	Float	relative frequency of reads sequenced from this transcript
10	AFREQ_SEQ	Integer	absolute number of reads sequenced from this transcript