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Old 06-19-2010, 04:25 AM   #2
Location: India

Join Date: Jun 2010
Posts: 20

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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