Dear Hong, The answer to your first questions is if there is no peak in the browser (no conservation score), it means that the score is 0 according to our analysis. In regards to the second question, we are unable to provide support for data analysis.
If you have any further questions, please don't hesitate to contact the mailing list again. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Harsha Rajasimha (NIH/NEI) [C]" <[email protected]> To: "[email protected]" <[email protected]> Cc: "Hong Hao (NIH/NEI) [E]" <[email protected]> Sent: Wednesday, July 21, 2010 8:49:24 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Questions to UCSC genome browser about conservation scores Dear UCSC support team, We use the various tools and visualizations offered by UCSC genome browser and are quite happy with it. We are trying to compare the conservation scores (from phastcons30way) for ~ 600 ChIP-seq peak sequences and ~ 600 random non-peak sequences. The ChIP-seq peak sequences are from stretches of genomic fragments (~500bp in length) within ChIP-seq peak regions. 1. When we exported conservation scores from UCSC genome browser, there are stretches of genomic regions without any conservation scores. Does this mean it is not available for this region or the score is vey low? Any suggestions on how to estimate 2. We would appreciate any suggestions / advice on how to randomly select non-peak regions to compare with conservation scores of peak sequences. Thanks for your time and help, Hong _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
