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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