Hi Jiwen,

This is a subject that has me very confused too. This thread at
seqanswer didn't help much either:
http://seqanswers.com/forums/showthread.php?t=8730

But it does have some good comments on the subject.

I did try using the two possible options I can think of:
fragment length - pair end read length - adaptor length

And:
fragment length - pair end read length

With the latter I get around 10% increase on properly paired reads. I
wonder if Tophat internally takes into account the adapters.

Still, it would be nice to get a definitive answer in this subject.

Regards,
Carlos

2012/3/6 杨继文 <jiwenyang0...@126.com>:
> Hi all,
>
> When mapping pair end RNA-seq reads using tophat, we need to type in "Mean
> Inner Distance between Mate Pairs".  In galaxy, we can read the following
> information:
>
> This is the expected (mean) inner distance between mate pairs. For, example,
> for paired end runs with fragments
>  selected at 300bp, where each end is 50bp, you should set -r to be 200.
> There is no default, and this parameter
>  is required for paired end runs.
>
> I think the size of fragment (here 300bp) includes not only the length of
> pair end reads, but also the length of adaptors. so, maybe the Mean Inner
> Distance between Mate Pairs should be : fragment length - pair end read
> length - adaptor length. Am I right? or did I miss something?
>
> Is it a must to type in the accurate value?
>
> Looking forward to your reply
>
> JIwen
>
>
>
>
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