I have some confusings about cufflinks output file:
1. Why the cufflinks output can match the isoforms but can not match the gene, like the first one:
Gm01 Cufflinks transcript 51481 61502 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373"; full_read_support "no";
Gm01 Cufflinks exon 51481 51625 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "1"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 51828 51925 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "2"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 52362 52465 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "3"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 52517 52571 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "4"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 52608 52639 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "
gene_id "CUFF.1"; transcript_id "PAC:16242891"; PAC:16242891 in the reference annotated file is the transform of gene Glyma01g00270.1? Can I recognise this gene CUFF.1 as Glyma01g00270, and those two transcripts belong to this gene?
2. I have noticed that many transcripts' FPKM value is 0.0000000000, should I exclude those transcripts? I suppose not. I just wondering wheather I need to set a FPKM cutoff after the output of cufflinks. Actually, even some transcript FPKM value is 0, it also can be significant expressed when using cuffdiff.
1. Why the cufflinks output can match the isoforms but can not match the gene, like the first one:
Gm01 Cufflinks transcript 51481 61502 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373"; full_read_support "no";
Gm01 Cufflinks exon 51481 51625 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "1"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 51828 51925 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "2"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 52362 52465 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "3"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 52517 52571 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "4"; FPKM "0.4311150338"; frac "1.000000"; conf_lo "0.045514"; conf_hi "0.816716"; cov "0.409373";
Gm01 Cufflinks exon 52608 52639 1000 - . gene_id "CUFF.1"; transcript_id "PAC:16242891"; exon_number "
gene_id "CUFF.1"; transcript_id "PAC:16242891"; PAC:16242891 in the reference annotated file is the transform of gene Glyma01g00270.1? Can I recognise this gene CUFF.1 as Glyma01g00270, and those two transcripts belong to this gene?
2. I have noticed that many transcripts' FPKM value is 0.0000000000, should I exclude those transcripts? I suppose not. I just wondering wheather I need to set a FPKM cutoff after the output of cufflinks. Actually, even some transcript FPKM value is 0, it also can be significant expressed when using cuffdiff.