running rseg WITH duplicated reads

[Andreas Gschwind]

Hi,

I've started using rseg recently and we're currently playing around
with removing duplicated reads from ChIP-seq analysis vs. not removing
them.

According to the manual, you should be able to turn off removing of
duplicated reads with th -j option, however I couldn't figure out how
this works. Also the -j option doesn't appear in rseg -help. Does that
mean, that the -j option isn't available anymore?

Thanks!

cheers, Andreas

[Song, Qiang]

Hi Andreas,

The "-j" option is hidden because my experience suggests removing duplicate 

reads by default works better.

However if you really would like to see the effect of removing vs. not removing,

The "-j" option can be made available by modifying the source code of rseg.cpp

and rseg-diff.cpp

For example, open rseg.cpp, find and uncomment the following lines:

//         opt_parse.add_opt("remove-jackpot", 'j', "Remove duplicate reads",

//                           false, Remove_Jackpot);

re-compile rseg. 

You will then able to change the "-j" option.

Regards,

Song Qiang

[Andreas Gschwind]

Cool, thanks!

On Feb 23, 7:14 am, "Song, Qiang" <qiang.s...@usc.edu> wrote:
> Hi Andreas,
>
> The "-j" option is hidden because my experience suggests removing duplicate
> reads by default works better.
>
> However if you really would like to see the effect of removing vs. not
> removing,
> The "-j" option can be made available by modifying the source code of
> rseg.cpp
> and rseg-diff.cpp
>
> For example, open rseg.cpp, find and uncomment the following lines:
>
> //         opt_parse.add_opt("remove-jackpot", 'j', "Remove duplicate
> reads",
> //                           false, Remove_Jackpot);
>
> re-compile rseg.
>
> You will then able to change the "-j" option.
>
> Regards,
> Song Qiang
>
> On Wed, Feb 22, 2012 at 3:01 AM, Andreas Gschwind

> <andreas.gschw...@unil.ch>wrote: