readTmap: reads output in .tmap format from cuffcompare
In psikon/cuffgo: cufflinks and GO analysis

Description Usage Arguments Format Value References

This function reads output from the cuffcompare specific tmap format. It is an tab delimited file that lists the most closely matching reference transcripts for each Cufflinks transcript.

1	readTmap(filename)

filename

location of the cuffcompare output file in .tmap format

Tab delimited file, where one row represents a Cufflinks transcripts with the following attributes:

Reference_gene_name: The gene_name attribute of the reference GTF record for this transcript, if present. Otherwise gene_id is used.
Referenc_transcript_id: The transcript_id attribute of the reference GTF record for this transcript
Class_code: The type of relationship between the Cufflinks transcripts and the reference transcript
Cufflinks_gene_id: The Cufflinks internal gene id
Cufflinks_transcript_id: The Cufflinks internal transcript id
FMI: Fraction of major isoform: the expression of this transcript expressed as a fraction of the major isoform for the gene. Ranges from 1 to 100.
FPKM: The expression of this transcript expressed in FPKM
FPKM_conf_lo: The lower limit of the 95% FPKM confidence interval
FPKM_conf_hi: The upper limit of the 95% FPKM confidence interval
coverage: The estimated average depth of read coverage across the transcript.
length: The length of the transcript.
major_isoform_ID: The Cufflinks ID of the gene's major isoform
ref_match_len: The length of the matching positions between the cufflinks and the reference transcript