anyone is using RepeatMasker to mask repeat sequence with short reads?

[feng]

Hi Is there anyone using RepeatMasker to identify repeat sequences?

It is normal to take a long time with 1M short reads?

or do you any suggestion on other tools that can remove human repeat sequences?

Thanks for any hint.

[bioinfosm]

why would you repeat mask the short reads?

Maybe you can repeat mask the human reference sequence? Or allow reads to map to n (small n for speed) max locations, and throw away those repeat mapped reads

[feng]

I want to use map these reads to a reference. These repeat sequences give a lot of hits without any conclusion.

[malachig]

If your goal is simply to identify reads that look like repeats and remove them from downstream analysis ... you could download a suitable set of repeat element sequences from RepBase and align your read sequences against these using a fast short read aligner such as BWA.