Thanks James! Actually, these annotations I'm working with I've generated with your dawgpaws pipeline :) The thing is, I was hoping to be able to curate them which is why I was wanting to use Apollo and gff3. Any idea on how I can work around this would be great!
Cheers, Elizabeth On Wed, May 12, 2010 at 7:44 PM, James Estill <[email protected]>wrote: > I think that if you do this is GFF2 format, it will work. All features will > need to have the same id (ie. LTR_model_01). > > If you have Gbrowse installed, you can display full annotations of LTR > retrotransposons using a glyph I wrote . Example images of the glyph are at > http://sourceforge.net/apps/trac/dawgpaws/attachment/ticket/35/cartoon_zoomed_out.pngand > http://sourceforge.net/apps/trac/dawgpaws/attachment/ticket/35/cartoon_zoomed_in.png > . > > The source for the gbrowse glyph is at > http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/trunk/gbrowse/glyph/ltr_simple.pm?revision=960 > > Unfortunately you can not curate annotations in Gbrowse, but it does allow > you to see the biology of the TE. > > -- Jamie Estill > -- [email protected] > -- http://jestill.myweb.uga.edu > -- http://www.epernicus.com/people/jestill > > > ----- Original Message ----- > From: elizabeth henaff > [mailto:[email protected]] > To: [email protected] > Sent: Wed, 12 May 2010 > 13:13:39 -0400 > Subject: Re: [apollo] parent - child tags for elements in > gff3 that are not genes > > > > Hi Ed, > > > > Thanks for your response. > > > > The data I have is such that I had one Parent (retrotransposon) with > > multiple children features (LTR, primer binding site, etc). It is > meaningful > > for me to retain these children features, so I was wondering of it would > be > > possible to circumvent the child-parent relationship by eliminating the > > Parent feature, and representing all its children as one discontinuous > > feature. > > I've tried to do that by adding an identical ID attribute to the children > > that belong together and "groupby : GENE" to the [type] definition but > when > > I load the gff3 I only see the first feature with a given ID. > > > > this is what I have added to gff3.tiers: > > > > [Tier] > > tiername : LTR_de_novo > > expanded : true > > labeled : true > > curated : true > > > > [Type] > > label : LTR_retrotransposon > > tiername : LTR_de_novo > > datatype : primer_binding_site > > datatype : RR_tract > > datatype : five_prime_LTR > > datatype : three_prime_LTR > > datatype : target_site_duplication > > datatype : transposon_fragment > > glyph : ThinRectangle > > color : red > > utr_color : 250,250,210 > > column : GENOMIC_LENGTH 1 > > column : GENOMIC_RANGE 1 > > column : SCORE > > column : NAME > > column : Source > > column : Strand > > > > and here's a snippet of the gff3 file: > > > > ##gff-version 3 > > MRGH6_contig ltr_finder:def three_prime_LTR 62941 64198 6 - . > > Name=three_prime_LTR; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_1 > > MRGH6_contig ltr_finder:def primer_binding_site 62841 62857 6 - . > > Name=primer_binding_site; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_1 > > MRGH6_contig ltr_finder:def RR_tract 56801 56815 6 - . Name=RR_tract; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_1 > > MRGH6_contig ltr_finder:def five_prime_LTR 55509 56766 6 - . > > Name=five_prime_LTR; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_1 > > MRGH6_contig ltr_finder:def primer_binding_site 105081 105103 6 - . > > Name=primer_binding_site; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_2 > > MRGH6_contig ltr_finder:def RR_tract 95013 95027 6 - . Name=RR_tract; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_2 > > MRGH6_contig ltr_finder:def five_prime_LTR 94168 95008 6 - . > > Name=five_prime_LTR; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_2 > > MRGH6_contig ltr_finder:def three_prime_LTR 105170 106020 6 - . > > Name=three_prime_LTR; > > Source=ltr_finder:def; Strand=-; ID=ltr_finder:def_ltr_finder_2 > > > > > > Thanks for your help! > > > > > > > > Elizabeth > > > > On Wed, May 12, 2010 at 6:15 PM, Ed Lee <[email protected]> wrote: > > > > > Hi Elizabeth, > > > > > > The only parent-child relationships that Apollo currently supports > > > is the gene-transcript-exon relationship. Unless you need to retain > > > the LTR relationship, I would suggest choosing the feature that > > > reflects the analysis best (either the parent or child) and then > > > removing the other (if removing the child, remember to remove the > > > "Parent" attribute in the GFF3 file). > > > > > > Cheers, > > > Ed > > > > > > > > > On Wed, 12 May 2010, elizabeth henaff wrote: > > > > > > Hello all, > > >> > > >> I'm trying to use Apollo to annotate transposable elements in some BAC > > >> sequences. I have run various prediction programs that generate data > in > > >> GFF3 > > >> format, and my idea is to load these results into Apollo to be able to > > >> manually curate them. > > >> > > >> > > >> The nature of the data is such that there are Parent-Child > relationships > > >> between features (as defined by the Parent=xxx tag in the 9th column), > > for > > >> example a three_prime_LTR feature would have as a Parent a > > >> LTR_retrotransposon feature, indicating that that LTR sequence belongs > to > > >> a > > >> particular retrotransposon. > > >> When I load the gff3 file into Apollo, I get the following error > > message: > > >> "only transcripts and exons can be children of annotations: > > >> three_prime_LTR[three_prime_LTR]" > > >> and a similar error message for each feature that has a Parent tag. > > >> Apollo then starts up, but only the features that do not have a Parent > > tag > > >> appear. > > >> > > >> In gff3.tiers I have defined a new [tier] as TE_annotation and a > [type] > > >> for > > >> each of the datatypes (the second column of the gff3 file) present in > my > > >> gff3 file. For each of the [type] fields I defined the > number_of_levels > > >> field as 3, but that doesn't seem to fix the problem. > > >> Any idea how I can resolve this? > > >> > > >> Thanks so much for any help! > > >> > > >> I've tried to attach the gff3, fasta and gff3.tiers files I'm using > but > > it > > >> seems like it makes the message too big, but I'd be happy to send them > if > > >> that would help. > > >> I'm running version 1.11.2 on ubuntu. > > >> > > >> Cheers, > > >> > > >> Elizabeth > > >> > > >> Centre de Recerca en AgriGenomica > > >> Barcelona, Espanya > > >> > > >> > > >
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