tophat -r mate inner distance option

[ssseq]

Hi,

When running tophat the -r or mate inner distance option is described as "the expected mean inner distance between mate pairs. For example, for paired end runs with fragments selected at 300 bp where each end is 50bp you should set -r to be 200."

The description makes me think that <r> is the distance after the adapters and the sequencing is accounted for e.g.

<adapter length - sequencing length - r - sequencing length - adapter length>

however, the example doesn't seem to take into account the length of both, thus making me think that this description is actually the length between the adapters e.g.

<adapter length - r - adapter length>

Could someone please confirm what is actually meant by this option?

Thanks,
Sarah

[simonandrews]

It must be the distance between the ends of the actual sequence which is generated. Tophat has no way to know how much stuff is in your library before the point at which your sequencing primers anneal.

[Daehwan]

Hi,

When running tophat the -r or mate inner distance option is described as "the expected mean inner distance between mate pairs. For example, for paired end runs with fragments selected at 300 bp where each end is 50bp you should set -r to be 200."

The description makes me think that <r> is the distance after the adapters and the sequencing is accounted for e.g.

<adapter length - sequencing length - r - sequencing length - adapter length>

however, the example doesn't seem to take into account the length of both, thus making me think that this description is actually the length between the adapters e.g.

<adapter length - r - adapter length>

Could someone please confirm what is actually meant by this option?

Thanks,
Sarah

Your example is correct, inner distance (in TopHat) = insert length - 2 * read length.