cufflinks: part of a cufflinks analysis
In psikon/cuffgo: cufflinks and GO analysis

Description Usage Format References

This data set give the first 1000 lines of a RNA-Seq experiment in human B lymphoma cells. The cufflinks suite was used to assemble the transcripts and search for differenly expressed genes. For the identification of the transcripts and exons the Ensembl annotations were used.

1	data(cufflinks)

A data frame with 1000 observations on the following 16 variables from a cufflinks run:

chr: Chromosome or contig name
program: The name of the program that generated this file
feature: The type of record (always either "transcript" or "exon"
start: The leftmost coordinate of this record
end: The rightmost coordinate of this record
score: The most abundant isoform for each gene is assigned a score of 1000. Minor isoforms are scored by the ratio (minor FPKM/major FPKM)
strand: Cufflinks' guess for which strand the isoform came from. Always one of "+", "-", "."
frame: deprecated - field not used
gene_id: Cufflinks gene id
transcript_id: Cufflinks transcript id
exon_number: number of exon for this transcript
fpkm: Isoform-level relative abundance in Fragments Per Kilobase of exon model per Million mapped fragment
frac: deprecated value
conf_lo: Lower bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, lower bound = FPKM * (1.0 - conf_lo)
conf_hi: Upper bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, upper bound = FPKM * (1.0 + conf_lo)
cov: Estimate for the absolute depth of read coverage across the whole transcript
full_read_support: When RABT assembly is used, this attribute reports whether or not all introns and internal exons were fully covered by reads from the data.