Homer repeat mask option turn off

I am using the findMotifsGenome.pl module for motif scanning and since my motif is a repeat sequence many of my sequences are not being scanned for since they are thrown out by homer due to masking , what would be the option to unmask the repeat sequences.

If not homer then which would be any other tool which would be good for scanning unmasked sequences?

motifscanner homer

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updated 4.4 years ago by Ram

• written 11.6 years ago by Aishwarya Kulkarni

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