Hi JIwen,
As the seqanswers thread shows, there is some debate about this. One of
the last posts there makes the most sense - where "fragment length" is
defined as the total genome bases covered by the aligned paired
sequences: tip of 5' start, through the gap, to the very 3' tail end and
where "mean inner distance" is the gap in the middle (between the paired
seqs) where there is no alignment. This could be tested with smaller
samples of data and compared to your fragment selection, to see how it
matches up. But, for a definitive answer, asking the tool authors is the
best bet. The contact information is: tophat.cuffli...@gmail.com
If you are given a reply that explains the calculation, it would be
great if the TopHat documentation itself were updated.
http://tophat.cbcb.umd.edu/manual.html
And we would be very glad to hear of the details, so that here at Galaxy
we could add the information to our RNA-seq help and the searchable
mailing list archives.
Great question! If we find out ourselves meanwhile, an update will be
posted back here to the mailing list,
Best,
Jen
Galaxy team
On 3/6/12 12:23 PM, 杨继文 wrote:
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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The Galaxy User list should be used for the discussion of
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