Hi everyone,
There seem to be a couple of threads that touch on this, but I'm not sure any answered this question... hope this is not a repeat:
I have mapped reads in tophat, and then used cufflinks to predict transcripts keeping a reference annotation in mind. I updated cufflinks today to 0.8.3
The gtf output from cuffcompare seems to be fine, for example:
But when I run cuffdiff: (cuffdiff .combined.gtf accepted_hits.sam accepted_hits.sam2)
the annotation information from the gtf is not output into the tracking file. I'm particularly interested in the nearest_ref_id.
Have I missed some option or something?
Thanks,
Chris
There seem to be a couple of threads that touch on this, but I'm not sure any answered this question... hope this is not a repeat:
I have mapped reads in tophat, and then used cufflinks to predict transcripts keeping a reference annotation in mind. I updated cufflinks today to 0.8.3
The gtf output from cuffcompare seems to be fine, for example:
Code:
Chr1 Cufflinks exon 24604 24768 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00011789"; exon_number "1"; oId "fam3.11.1"; nearest_ref "ENSTGUT00000004895"; class_code "e"; tss_id "TSS1"; Chr1 Cufflinks exon 25776 25957 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00011789"; exon_number "2"; oId "fam3.11.1"; nearest_ref "ENSTGUT00000004895"; class_code "e"; tss_id "TSS1";
the annotation information from the gtf is not output into the tracking file. I'm particularly interested in the nearest_ref_id.
Code:
tracking_id class_code nearest_ref_id gene_short_name tss_id locus q0_FPKM q0_conf_lo q0_conf_hi q1_FPKM q1_conf_lo q1_conf_hi XLOC_000001 - - - ,TSS1 Chr1:24603-28303 1.09128 0 2.93506 4.9699 0.545109 9.39469 XLOC_000002 - - - TSS2,TSS3 Chr1:639605-651348 32.5089 26.6549 38.3628 30.8267 25.9758 35.6777
Thanks,
Chris
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