Hi Han, Thank you for bringing this to our attention. We were able to find and fix the problem by this morning. Please let us know if you find any other problems on our website by emailing genome at soe.ucsc.edu.
Additionally, it might be of interest to you that we are planning another update of the data shortly that will improve the display of the track when zoomed in at the base level. The update should be available within a few weeks. Thank you, Mary --------------------- Mary Goldman UCSC Bioinformatics Group On 6/10/10 9:19 AM, Ann Zweig wrote: >> Subject: >> question about genome browser hg18 >> From: >> XU Han <[email protected]> >> Date: >> Thu, 10 Jun 2010 11:33:15 +0800 >> To: >> "'[email protected]'" <[email protected]>, >> "'[email protected]'" <[email protected]> >> >> To: >> "'[email protected]'" <[email protected]>, >> "'[email protected]'" <[email protected]> >> CC: >> WEI Chia-Lin <[email protected]> >> >> >> Dear Sir: >> >> >> >> I’m Xu Han from Genome Institute of Singapore. I’m writing regarding >> the inconsistency of ChIP-seq peak view and signal view, based on >> hg18 assembly. >> >> >> >> Today I opened the CTCF track (regulation->broad histone) in hg18. I >> used the configuration as follow: >> >> Auto-scale to data view, always include zero on, no log transformation. >> >> >> >> As the result, the genome browser showed the figure as attached. To >> my surprise, I found that the peak view and signal view are not >> consistent for “GM12878 CTCF S” track. For example, the signal view >> showed a peak around chr4:174330000 (red circle), but the peak view >> didn’t show any peak there; on the other hand, peak view suggested a >> peak around chr4:174450000, but there is no significant signal based >> on signal view. In addition, the intensity of signal (Y axis) looks >> pretty low (<1.5), which is unusual for a CTCF ChIP-seq library based >> on my experience. >> >> >> >> I recalled that these problems were not observed when I looked at the >> same track and the same loci a couple of months ago. I wonder if >> there has been any updating of the tracks recently. If so, these >> problems may be associated with the new version. Could you take a >> check on the problems? >> >> >> >> Thank you very much and I’m looking forward to your reply. >> >> >> >> Han >> >> >> >> >> >> Xu Han | Senior Bioinformatics Specialist | Computational and >> Mathematical Biology | Genome Institute of Singapore | Tel: 64788195 >> | Fax: 64789058 | Warning: This message may contain confidential >> information. If sent in error, please notify me and delete the email. >> Thank you. | >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
