Difference between mate pair and pair end

[bassu]

Hi All,

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

Thanks

[Brajbio]

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]

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