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Re: [Gmod-ajax] AJAX Gbrowse - problem rendering tiles for EST reads
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From: Mitch S. <mit...@be...> - 2007-12-05 08:55:32
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It's tough to say; I don't know of a reason why this wouldn't work, and I'm sure there are lots of possibilities for what's going on. So I'd like to go through a bit of troubleshooting, if you don't mind answering some questions. 1. What output (if any) do you get when you try to generate tiles? 2. Can you generate tiles for other kinds of features? 3. What database are you using (Bio::DB:GFF, Bio::DB::SeqFeature::Store, Chado, ?) 4. What versions of Bioperl and GBrowse are you using? Thanks, Mitch Davis, Adam Christiaan wrote: > I have been having problems getting the tile generator to generate tiles for EST reads. I have them set up with EST DNA fasta files so that when zoomed in it displays the DNA with insertions/deletions and mismatches. It all displays perfectly fine in gbrowse, but when I try to generate tiles, it hangs and never even starts the entire landmark view. I tried disabling the DNA display when zoomed in, but it still wouldnt generate. I'm wondering if it has to do with having the GFF file set up to utilize the DNA fasta file for the EST reads. For all of this, I loaded everything into database first, then generated tiles after checking that it displayed properly in gbrowse. Here are some example lines from my EST gff file > > scaffold_45 est match 753297 756343 . + . Target EST:CACW5781.b1 1 905 > scaffold_30 est match 563618 564742 . - . Target EST:CACW6759.g1 1 742 > scaffold_2 est match 1281895 1282741 . - . Target EST:CACW11451.g1 1 863 > scaffold_68 est match 160772 161720 . + . Target EST:CACW4784.g2 1 725 > scaffold_45 est HSP 753297 753324 . + . Target EST:CACW5781.b1 1 28 > scaffold_45 est HSP 753463 753501 . + . Target EST:CACW5781.b1 29 67 > scaffold_45 est HSP 753854 753979 . + . Target EST:CACW5781.b1 68 193 > scaffold_45 est HSP 754933 755079 . + . Target EST:CACW5781.b1 194 340 > scaffold_45 est HSP 755505 755688 . + . Target EST:CACW5781.b1 341 524 > scaffold_45 est HSP 755963 756343 . + . Target EST:CACW5781.b1 525 905 > scaffold_30 est HSP 563618 564293 . + . Target EST:CACW6759.g1 1 675 > scaffold_30 est HSP 564676 564742 . + . Target EST:CACW6759.g1 676 742 > scaffold_2 est HSP 1281895 1282741 . - . Target EST:CACW11451.g1 1 863 > scaffold_68 est HSP 161163 161720 . - . Target EST:CACW4784.g2 1 560 > scaffold_68 est HSP 160772 160936 . - . Target EST:CACW4784.g2 561 725 > > And here is the track in my conf file: > [EST] > feature = match:est > glyph = segments > label_position = left > draw_target = 1 > show_mismatch = 1 > fontcolor = blue > mismatch_color = red > true_target = 1 > realign = 1 > bgcolor = white > fgcolor = black > key = ESTs > > [EST:1000] > label_position = top > > I have tried commenting out most of the track settings trying to make it just a generic track, and it still doesnt work, which is why I think it has to do with the GFF file formatting. > > If anyone can possibly provide any insight as to why I can't get the tiles to generate (or if it just isn't supported), I would greatly appreciate it. > > -Adam Davis > > ------------------------------------------------------------------------- > SF.Net email is sponsored by: The Future of Linux Business White Paper > from Novell. From the desktop to the data center, Linux is going > mainstream. Let it simplify your IT future. > http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
