Hello Jiwen, It is possible to view both the TopHat and Cufflinks output together in Trackster. Are you doing this? Are you seeing that reads/transcripts are spanning the splice regions (align to one side, span the gap, then align to the other side)? This is what would be expected for RNA-seq data. It might help to import a known transcript track from UCSC or Biomart and visualize that, to get a better understanding of how genomic features are represented in the Trackster UI. If you have an error dataset from an RNA-seq tool, you can send in a bug report, but that doesn't seem to be the case. Rather, there is a question about how the calculation are done. For cases like that, the tool authors might be the best source for help. Contact info is in this wiki link "Example: unexpected results with RNA-seq analysis tools." http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result Hopefully this helps, Best, Jen Galaxy team On 2/3/12 7:24 AM, 杨继文 wrote:

Dear all, Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using "visaulization" function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought "splice junction" is calculated from the mapped reads. However, I think cufflinks only uses "accepted hits" as input, maybe it is not a big problem that "splice junction' is not accurate. Am I right? Was there something wrong when I mapped my reads with tophat? Hope you can help me figure it out. Looking forward to hearing from you. Jiwen

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