How to Repeatmask sequence files >100kb

[Neilyoungson]

I'd like to find out the repeat content (LINES, SINES, LTR-retrotransposons etc) of my Illumina HiSeq sequence Bam files.

Repeatmasker's online search takes only up to 100kb of sequence and running a local version requires command-line skills (I'm not a bioinformatician).

Does anyone know of a way to do this without command-line skills?

Cheers,
Neil

[SES]

I would encourage you to try the command line version because you will have a lot more flexibility and the commands are quite easy. In the simplest case:

RepeatMasker seqs.fas

Using a custom library for masking is simple as saying "-lib file_of_repeats.fas" and specifying a single species to use for masking is also possible by saying "-species human" to mask human repeats, for example.

[GenoMax]

I'd like to find out the repeat content (LINES, SINES, LTR-retrotransposons etc) of my Illumina HiSeq sequence Bam files.

Repeatmasker's online search takes only up to 100kb of sequence and running a local version requires command-line skills (I'm not a bioinformatician).

Does anyone know of a way to do this without command-line skills?

Cheers,
Neil

This is where you call upon a friend who has the necessary skills, if you truly do not wish to do it on your own.

Like SES said this would be simple to do on the command line .. provided you had access to the necessary resources/time to pick up some basic unix skills.

[Neilyoungson]

Thanks guys,
it seems that I've reached that crossroads, and it is now time to learn some unix.
Wish me luck.
Neil

[GenoMax]

Thanks guys,
it seems that I've reached that crossroads, and it is now time to learn some unix.
Wish me luck.
Neil

That's the spirit.

Start here: http://korflab.ucdavis.edu/unix_and_Perl/

[SES]

That's the spirit.

Start here: http://korflab.ucdavis.edu/unix_and_Perl/

Very nice! I was about to post the same link but you beat me to it.

Note that this is also now a published book you can get on Amazon, or any other bookstore I'm sure.