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-   -   Difference between mate pair and pair end (http://seqanswers.com/forums/showthread.php?t=5596)

bassu 06-19-2010 04:48 AM

Difference between mate pair and pair end
 
Hi All,

i am confused between two terminology Mate paired and Pair end. Please help me out on this.

Thanks

Brajbio 06-19-2010 05:25 AM

Even i have a doubt regarding 'mate-pair inner distance' parameter option -r which is essential to give while running tophat with pair-ends.

Can someone help me how to determine the mate-inner-dist (-r) if i know the reads size but not the fragment size.
For example if my reads length (paired-reads) is of length 50 bp and in another set the reads length (paired-reads) is 45 bp.

kmcarr 06-19-2010 07:13 AM

Quote:

Originally Posted by bassu (Post 20466)
Hi All,

i am confused between two terminology Mate paired and Pair end. Please help me out on this.

Thanks

A search of the forum reveals this thread http://seqanswers.com/forums/showthr...ight=Mate+pair


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