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Hi,
I've aligned RNA-Seq PE reads to X.laevis unigene EST database and have generated DE gene lists with cuffdiff. I assumed that there was no annotation file but have just noticed that the .fa file contains annotation in the scaffold (expressed gene) name. For example:
gnl|UG|Xl#S14232313 Xenopus laevis hypothetical protein MGC52983, mRNA (cDNA clone MGC:52983 IMAGE:4930778), complete cds /cds=p(53,1054) /gb=BC046667 /gi=28302290 /ug=Xl.7 /len=18
91
However, when I use this .fa file for cufflinks/cuffdiff only the first part of the name gets carried over as 'gene' column in the cuffdiff output file gene_exp.diff. e.g.
gnl|UG|Xl#S28473480:69-1962
Is there any way to ensure the entire name gets carried over to help make sense of the gene lists generated in cummerbund?
Any help would be very welcome!
Best,
N
I've aligned RNA-Seq PE reads to X.laevis unigene EST database and have generated DE gene lists with cuffdiff. I assumed that there was no annotation file but have just noticed that the .fa file contains annotation in the scaffold (expressed gene) name. For example:
gnl|UG|Xl#S14232313 Xenopus laevis hypothetical protein MGC52983, mRNA (cDNA clone MGC:52983 IMAGE:4930778), complete cds /cds=p(53,1054) /gb=BC046667 /gi=28302290 /ug=Xl.7 /len=18
91
However, when I use this .fa file for cufflinks/cuffdiff only the first part of the name gets carried over as 'gene' column in the cuffdiff output file gene_exp.diff. e.g.
gnl|UG|Xl#S28473480:69-1962
Is there any way to ensure the entire name gets carried over to help make sense of the gene lists generated in cummerbund?
Any help would be very welcome!
Best,
N
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