Hello, Apologies for the multiple emails, I am still trying to figure out how stranding of the mRNAs is determined in the genome browser. More specifically, how is stranding determined for those mRNAs that have a 0 in the mrnaOrientInfo table?
Thank you for your help, Nandita On Thu, Jan 15, 2009 at 2:46 PM, Nandita Garud <[email protected]> wrote: > Hello, > > I am trying to understand how strand information for mRNAs in the all_mrna > table is determined. I have followed the FAQ about estOrientInfo, and am I > correct in understanding that if the intronOrientation field is negative, > then the strand orientation should actually be opposite of what is listed in > the all_est table? Is this the same for the mRNAs? How is orientation in the > all_mrna table determined in the first place? Is it based on the orientation > suggested by the one who submitted the mRNA to the database, but then > possibly revised in the mrnaOrientInfo table? If the intronOrientation is 0 > in the mrnaOrientInfo table, how probable would it be that the orientation > suggested by the all_mrna table is correct? > > Thank you, > > Nandita > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
