cuffmerge: part of a cufflinks analysis

In psikon/cuffgo: cufflinks and GO analysis

Description

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.

Usage

data(cuffmerge)

Format

A data frame with 1000 observations on the following 16 variables from a cuffmerge 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

gene_name

The gene_name attribute of the reference GTF record for this transcript, if present. Otherwise gene_id is used.

oId

old identifier of this gene e.g. in cufflinks output

contained_in

is this transcript contained in a nother bigger transcript

nearest_ref

The reference transcript to which the class code refers, if any

class_code

The type of relationship between the Cufflinks transcripts and the reference transcript

tss_id

The tss_id associated with the object, or "-" if not a transcript/primary transcript, or if tss_id isn't present

References

Cuffmerge Output:http://cufflinks.cbcb.umd.edu/manual.html#merger_output

psikon/cuffgo documentation built on May 26, 2019, 10:32 a.m.