RepeatMasker annotation

The repeat annotation file is generated from the ouput of RepeatMasker [14]. Users can use our custom scripts to create repeat gff3 file either from UCSC genome browser or from local RepeatMasker output, which are detailed in readme file in annotation/prepareAnnotation folder

There are a list of special feature attributions in repeat annotation files. The "repName","repClass" and "repFamily" features indicate the name, class and family of the repeat respectively. The other three features are used to indicate the location of repeat region in consensus sequence.

Example of "attributes" column:

repName=L1_Mur2;repClass=LINE;repFamily=L1;repSt=1413;repEnd=1567; repFullLen=5877;

Chongjian Chen 2012-01-26