Feedback for building Drosophila GTF annotation

[dsturgill]

I'm working on generating a GTF version of current Flybase annotation for Drosophila, since this would include recent transcript models absent in Ensembl GTFs. I want to confirm it is stable with all the commonly used analysis tools, and make this available to the broader community, so I'd like to solicit opinions on the following:

- Other than including tss_id and p_id attributes, are there any aspects of a GTF annotation that you would like to see, or pitfalls to watch for? (Such as antisense transcript models that cause GTF parsing errors)

- Do you have any suggestions about handling polycistronic genes (where transcripts have identical coordinates but non-overlapping CDS, and hence different gene_ids), to avoid confusion when reporting gene-level results?

- Are there any tools other than Cufflinks/Tophat that you would like to ensure the GTF works correctly with?

Thanks for any feedback!

Dave

[FLYINGDOLPHIN]

Hello,

I am trying to make an annotation files for the transportable elements in drosophila, which is not included in the normal annotation file. Can you give me some detail instruction as to how to make it?

Thanks.
F