Hi all,
I am confused by the Illumina iGenomes annotation downloaded from (http://cufflinks.cbcb.umd.edu/igenomes.html).
I downloaded the hg19 annotation under data source "UCSC" and I used the genes.gtf in the annotation folder as the reference to cufflinks/cuffdiff. I found that this annotation is most likely to be the refSeq annotation instead of the UCSC annotation. However, for some genes, such as TP53, the iGenome annotation has 7 transcripts while refSeq has 8 transcripts. Please look at the screenshot: the top panel is the iGenome annotation and the lower is the refSeq annotation. It is easy to see that the last third transcript is not included in iGenome annotation.
I wonder if I misunderstand the iGenome resource.
Could any one help to clarify which annotation(refSeq, genCode, UCSC) is it?
I am confused by the Illumina iGenomes annotation downloaded from (http://cufflinks.cbcb.umd.edu/igenomes.html).
I downloaded the hg19 annotation under data source "UCSC" and I used the genes.gtf in the annotation folder as the reference to cufflinks/cuffdiff. I found that this annotation is most likely to be the refSeq annotation instead of the UCSC annotation. However, for some genes, such as TP53, the iGenome annotation has 7 transcripts while refSeq has 8 transcripts. Please look at the screenshot: the top panel is the iGenome annotation and the lower is the refSeq annotation. It is easy to see that the last third transcript is not included in iGenome annotation.
I wonder if I misunderstand the iGenome resource.
Could any one help to clarify which annotation(refSeq, genCode, UCSC) is it?
Comment