Configuring REannotate Apollo Tiers Files on OSX

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Posted 23 Jun 2009 in genome bioinformatics, OSX hacks, transposable elements

Vini Pereira has recently published a nice paper on his REannotate package for defragmenting pieces of dead and nested transposable elements (TEs) detected using RepeatMasker. Defragmentation is an important aspect of accurately annotating and data mining transposable elements (as Hadi Queseneville and I have discussed in our 2007 review article on TE bioinformatics resources).

One of the nice features of REannotate is the ability to output GFF files ready for import into the Apollo genome annotation and curation tool. Although there is excellent documentation for configuring Apollo and REannotate provides a custom “tiers” file to properly display defragmented TE annotations, I struggled a bit to get these to work together on OSX based on the REannotate documentation. Partly my difficulty arose because the location of the “conf/” directory for the Apollo installation on OSX is not explicit, and in the end finding this directory provided two alternate solutions to this problem. Both solutions assume Apollo was installed via the .dmg file

Solution 1: This solution should be platform independent of the location of the conf/ directory.

$cd $HOME/.apollo
$wget -O ensj.tiers http://www.bioinformatics.org/reannotate/download/REannotate.tiers
Launch Apollo
Import REannotate GFF file and associated FASTA sequence.
Select File->Save Type Preferences..
Save As: ensj.tiers

Solution 2: This solution is OSX specific, and depends on the location of the conf/ directory.

$cd $HOME/.apollo
$wget -O REannotate.tiers http://www.bioinformatics.org/reannotate/download/REannotate.tiers
$cat /Applications/Apollo.app/Contents/Resources/app/conf/ensj.tiers REannotate.tiers > ensj.tiers
Launch Apollo
Import REannotate GFF file and associated FASTA sequence.

One final note: I find it helpful to “grep -v un-RepeatMasked_sequence” the REannotate GFF files before loading into Apollo to get rid of non-RepeatMasked annotations.


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