Hi Mike, If you look at this session here: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Marygoldman&hgS_otherUserSessionName=dm3CG32491-RVgene, you will see the 7 genes in the flyBaseGene table where strand is "." instead of "+" or "-". These genes are marked as the strand being unknown by the absence of directional arrows in the introns. The lack of strand information for these genes is consistent with what is reported on flyBase.org.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 1/4/11 12:36 PM, Michael Muratet wrote: > Dear Colleagues > > I just downloaded the flyBaseGene table in gtf format and found 79 > features where the strand equals ".". The gene names are CG32491-R? > where ? is T through Z. The original table appears to have the same > field: > > #filter: flyBaseGene.name = 'CG32491-RV' #bin name chrom strand > txStart txEnd cdsStart cdsEnd exonCount exonStarts > exonEnds > 716 CG32491-RV chr3R . 17194101 17203121 > 17194594 17202748 5 > 17194101,17200781,17202323,17202540,17203009, > 17194784,17201634,17202463,17202798,17203121, > The browser shows the features on the negative strand. > Should the strand field be '-'? > Thanks > Mike > > > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > [email protected] > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
