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Old 06-19-2010, 03:48 AM   #1
bassu
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Default 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
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Old 06-19-2010, 04:25 AM   #2
Brajbio
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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.
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Old 06-19-2010, 06:13 AM   #3
kmcarr
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Quote:
Originally Posted by bassu View Post
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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