a little help with creating annotations out of lower case bases

[teetee1]

I recently noticed that UCSC genome data such as the one for C. elegans below (30MB file)

http://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/chromFa.tar.gz

contains lower case bases in the sequence for repeats or low complexity regions. I would like to mask them out for my mapping or variant calling by creating annotations out of those regions.

The only two format I can think of are BED and GFF but I wonder if anyone has a better idea on how to do that or if there is already an existing tool on UCSC / other tools to do so. TIA.

[Brian Bushnell]

Not sure if this is exactly what you want, but BBTools contains a script that will convert lower-case letters to Ns:

reformat.sh in=reference.fasta out=masked.fasta lowercaseton

It works on gzipped files but not on tar archives, so you'll have to untar it first.