Hi Weimin, We can only guide you on how to use the browser and are unable to provide assistance with how you use the data. Best of luck!
Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: dongdong zhaoweiming <[email protected]> Date: Tue, Dec 13, 2011 at 7:24 AM Subject: [Genome] gene-intron-pig To: [email protected] Hi, I had a RNA-Seq data in pig muscle tissue and assembled my sequence using trinity, then I want to see how many sequence was overlapped with pig gene intron, I first downloaded the position of each pig gene from NCBI based on the sus genome 10.2 and BLAT my sequence vs sus genome 10.2. You said that when a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. However, some sequence have mutipostion that don't have a bese identity level within 0.5% but have 95% identity and 90% of their length, so should I take all the mutiposition that just meet 95% identity and 90% of their length or the mutiposion that meet your criterion to aganist the position of pig gene from NCBI? Thanks a lot! Best Wishes! weimin zhao _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
