Good Evenin Jyoti:
I guess it depends upon where you obtained the nib files from ?
What nib files are you using and how do you operate the command ?
The option -masked does the following:
-masked - use lower case characters for bases meant to be masked out
which means it prints lower case characters in masked regions.
What do you mean "not able to repeat mask sequence" ?
Are you trying to run RepeatMasker ?
--Hiram
Shah, Jyoti K. wrote:
> Hi UCSC team,
>
> I am using your nibFrag tool to extract parts of a sequence. I am not
> able to repeat mask sequences using you 'masked' or 'hardMasked'
> options. Do they really mask the sequence or they just ignore the parts
> of sequence that have been pre-masked?
>
> Thanks
> Jyoti
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