I ran cufflinks on several BAM files and get tracking.gtf files looking like (truncated lines):
and then run cuffcompare to compare with a merged gtf file as
but, the myprefix.tracking only gives me FPKM estimates equal zero for all genes:
note that CUFF.8 in the transcripts.gtf has a non-zero FPKM estimate but this does not propagate to the myprefix.tracking file.
Any ideas why? Grateful for answers.
Code:
Chr1 Cufflinks transcript 22746 23685 1000 + . gene_id "CUFF.8"; transcript_id "CUFF.8.1"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "52.362831"; Chr1 Cufflinks exon 22746 23020 1000 + . gene_id "CUFF.8"; transcript_id "CUFF.8.1"; exon_number "1"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "$ Chr1 Cufflinks exon 23096 23685 1000 + . gene_id "CUFF.8"; transcript_id "CUFF.8.1"; exon_number "2"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "$ Chr1 Cufflinks transcript 79944 80186 1000 + . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "3077.9273423595"; frac "1.000000"; conf_lo "1765.494714"; conf_hi "4390.359971"; cov "2714.84$ Ch
Code:
cuffcompare -o myprefix -r merged.gtf transcripts.gtf
Code:
TCONS_00000001 XLOC_000001 XLOC_000001|TCONS_00000001 c q1:CUFF.8|CUFF.8.1|100|0.000000|0.000000|0.000000|0.000000|- TCONS_00000002 XLOC_000002 XLOC_000002|TCONS_00000002 = q1:CUFF.11|CUFF.11.1|100|0.000000|0.000000|0.000000|0.000000|- TCONS_00000003 XLOC_000003 XLOC_000003|TCONS_00000003 = q1:CUFF.2|CUFF.2.1|100|0.000000|0.000000|0.000000|0.000000|- TCONS_00000004 XLOC_000004 XLOC_000004|TCONS_00000004 = q1:CUFF.4|CUFF.4.1|100|0.000000|0.000000|0.000000|0.000000|- TCONS_00000005 XLOC_000005 XLOC_000005|TCONS_00000006 c q1:CUFF.16|CUFF.16.1|100|0.000000|0.000000|0.000000|0.000000|- T
Any ideas why? Grateful for answers.
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