SEQanswers - View Single Post - Difference between mate pair and pair end

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.

06-19-2010, 05:25 AM	#2
Brajbio Member 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.