View source: R/repbase.clean.R
repbase.clean | R Documentation |
Clean the headers of the Repbase fasta files so that headers can be used to create a blast-able database.
repbase.clean(repbase.file, output.file)
repbase.file |
fasta file storing the corresponding Repbase annotation, e.g. |
output.file |
name/path of the cleaned Repbase annotation file. |
The Repbase database can be downloaded after registration at http://www.girinst.org/repbase/.
The corresponding files as they are however, cannot be converted into a blast-able database.
Hence, a pre-filtering step is neccessary to be able to use this database with the e.g. repbase.query
function.
Hajk-Georg Drost
http://www.girinst.org/repbase/
## Not run: # PreProcess Repbase: A thaliana # and save the output into the file "Athaliana_repbase.ref" repbase.clean(repbase.file = "athrep.ref", output.file = "Athaliana_repbase.ref") ## End(Not run)
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