(cc'ing back to galaxy-user because this information may be useful to
others)
The problem is that the reference gene annotation that you're using,
RefGene from UCSC, has an error. Specifically, a transcript_id
attribute is duplicated for two different transcripts, one on chr1 and
one on chr19:
--
chr1 Cufflinks transcript 34611 36081 1 -
. gene_id "NR_026818"; transcript_id "NR_026818"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr1 Cufflinks exon 34611 35174 1 - .
gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "1"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr1 Cufflinks exon 35277 35481 1 - .
gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "2"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr1 Cufflinks exon 35721 36081 1 - .
gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "3"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr19 Cufflinks transcript 76220 77690 1 -
. gene_id "NR_026818"; transcript_id "NR_026818"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr19 Cufflinks exon 76220 76783 1 - .
gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "1"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr19 Cufflinks exon 76886 77090 1 - .
gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "2"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
chr19 Cufflinks exon 77330 77690 1 - .
gene_id "NR_026818"; transcript_id "NR_026818"; exon_number "3"; FPKM
"0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi
"0.000000"; cov "0.000000";
--
When trying to visualize either the reference annotation or Cufflinks
datasets created using this annotation, an error occurs because Galaxy
tries to reconcile these two transcripts. More graceful error handling
is planned.
To avoid this error, use the iGenomes reference available in the
iGenomes data library (hg19 and mm9 only right now). There are other
benefits to this annotation as well; it has additional attributes
useful for Cuffdiff. I was able to visualize your Cufflinks data, as
well as the iGenomes gene annotation, using Trackster.
Best,
J.
