Cufflinks GTF file

ECHo · 02-15-2010, 03:59 AM

The following is excepted from my gtf file, which is produced by Cufflinks:

chr21 Cufflinks transcript 14304464 14305055 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970";
chr21 Cufflinks exon 14304464 14304509 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; exon_number "1"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970";
chr21 Cufflinks exon 14304969 14305055 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; exon_number "2"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970";
chr21 Cufflinks transcript 14305973 14306356 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000";
chr21 Cufflinks exon 14305973 14306002 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; exon_number "1"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000";
chr21 Cufflinks exon 14306312 14306356 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; exon_number "2"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000";

The "+" and "." forms mean "strand" and "frame".
But how could "+/-/." express strand?
Does "+" mean the "start-to-end" order and "-" mean "end-to-start" order?
And how about "."?
After searching, some other GTF files use "0/1/2" to express frame; however, Cufflinks uses "+/-/." to express.
Do they match the same meanings?

Thanks.

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02-15-2010, 03:59 AM	#1
ECHo Member Location: Taiwan Join Date: Jan 2010 Posts: 17	Cufflinks GTF file The following is excepted from my gtf file, which is produced by Cufflinks: chr21 Cufflinks transcript 14304464 14305055 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970"; chr21 Cufflinks exon 14304464 14304509 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; exon_number "1"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970"; chr21 Cufflinks exon 14304969 14305055 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; exon_number "2"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970"; chr21 Cufflinks transcript 14305973 14306356 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000"; chr21 Cufflinks exon 14305973 14306002 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; exon_number "1"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000"; chr21 Cufflinks exon 14306312 14306356 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; exon_number "2"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000"; The "+" and "." forms mean "strand" and "frame". But how could "+/-/." express strand? Does "+" mean the "start-to-end" order and "-" mean "end-to-start" order? And how about "."? After searching, some other GTF files use "0/1/2" to express frame; however, Cufflinks uses "+/-/." to express. Do they match the same meanings? Thanks.