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Dear All,
I have have observed this strange thing in analyzing the Cuffdiff results:
there are some genes evidently different but with a small overlap (generally the final exon of one is overlapping with the first exon of the other one): they are annotated with the same xloc. Just to give an example in my case :
grep "CCDC51" genes.fpkm_tracking
XLOC_038619 - - XLOC_038619 CCDC51,RP11-24C3.2 TSS84938,TSS84939,TSS84940 chr3:48473573-48481529 - - 5.74368 4.08119 7.40618 OK 7.11625 4.60213 9.63036 OK 6.30723 4.33648 8.27799 OK
Although I expected to find these genes with different Xloc the strange fact is that when I look in isoform_exp.diff I find the isoforms relative to both genes, viceversa looking in gene_exp.diff I find only one of the two genes. How this is possible?
Thanks in advance
Luigi
I have have observed this strange thing in analyzing the Cuffdiff results:
there are some genes evidently different but with a small overlap (generally the final exon of one is overlapping with the first exon of the other one): they are annotated with the same xloc. Just to give an example in my case :
grep "CCDC51" genes.fpkm_tracking
XLOC_038619 - - XLOC_038619 CCDC51,RP11-24C3.2 TSS84938,TSS84939,TSS84940 chr3:48473573-48481529 - - 5.74368 4.08119 7.40618 OK 7.11625 4.60213 9.63036 OK 6.30723 4.33648 8.27799 OK
Although I expected to find these genes with different Xloc the strange fact is that when I look in isoform_exp.diff I find the isoforms relative to both genes, viceversa looking in gene_exp.diff I find only one of the two genes. How this is possible?
Thanks in advance
Luigi