Phagealign for Paired-End analysis

[cbasel]

Hi everybody,
is it possible to use Phagealign for Paired-End analysis? I know it is much slower than Eland and so on...But we would like to compare the results for a specific application which deals with a very small genome. If it is possible, what would be the right GERALD parameter (For Eland it is "ANALYSIS eland_pair")?
Thanks and best,
Chris

[seq_GA]

Did u try using

ANALYSIS default

? I haven't used it but looks like the same for Single as well as pair end.

[dcjamison]

No, you cannot use phageAlign for paired ends -- the pairing scripts run off the eland_multi output and will not accept the phageAlign output. You can however analyze each end separately -- do an "ANALYSIS default" run with "USE_BASES as Y36N36 and then a second run with N36Y36.

[cbasel]

Thanks a lot for your replies.
Chris