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  • .PRO Transcriptome Profile

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Section

The Profile (.PRO) format is designed to describe the simulated characteristics of each transcript from the reference annotation, one per line. After each step of a simulation run, tab-separated are added to the file.

Column NrNameValueDescription
1Locuschrom:start-end[W|C]identifier of the transcriptional locus, given by the chromosome (chrom), start respectively end position, and the strand (Watson or Crick).
2Transcript_IDStringtranscript identifier from the reference annotation.
3Coding[CDS|NC]specifies whether the transcript has an annotated coding sequence (CDS) or not (NC)
4LengthIntegerthe mature length of the transcript after splicing out introns, disregarding the poly-A tail, as annotated in the reference annotation
5Expressed FractionFloatfraction of RNA molecules that represent transcripts that are qualitatively equal to this RNA form
6Expressed NumberIntegerabsolute number of expressed RNA molecules
7Library FractionFloatfraction of cDNA molecules in the final library that have been produced from this transcript
 Library NumberIntegerabsolute number of cDNA fragments generated from this transcript
9Sequenced FractionFloatfraction of total reads that have been sequenced from this transcript
10Sequenced NumberIntegerabsolute number of reads sequenced from this transcript
11Covered FractionFloatfraction of the transcript that is covered by reads
12Chi SquareIntegerchi-square goodness of fit measurement of coverage uniformity
13Coefficient of VariationFloatcoefficient of variation for transcript coverage