Masked or unmasked genome for ChIP-seq analysis?

[hbbio]

Should I use the masked genome or not (chromFaMasked vs. chromFa; both from UCSC) to align my chIP-seq data? If it depends on the alignment programs? Thanks!

[apfejes]

I would think this would depend on the aligner you're using, and what you plan to do with multi-match reads.

Depending on what you've precipitated in your ChIP, You're probably more interested in unique regions, anyhow, so I don't think it will make a big difference for the most part. If you were working with whole genome or wtss, I would expect it to have a bigger impact.

[Chipper]

Definitely unmasked. The repeats masked by repeatmasker (alu, line, sine, mir etc) do contain unque sequences, and probably using masked reference would lead to false alignments of reads from repeats if you allow several mismatches. chr.fa files are also repeatmasked but to lowercase rather than N:s so this information can still be used by some aligners-

[apfejes]

If you're allowing multiple matches in a ChIP-Seq experiment, how are you interpreting them?

Anthony