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Old 05-24-2013, 06:34 AM   #1
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Location: new delhi

Join Date: May 2013
Posts: 4
Default How are mate pairs formed and stored

Lets say I have a genome G=ACTTAGGCTA. So mate pairs as far as I know are two reads in the genome which are separated by a known distance. Consider read length of 3 and insert size or distance as 4 so will the read CTT will be paired with GGC or its reverse complement GCC?
Also with what the read GCT be paired because the genome length is over after adding distance 4?
Also with reference to the read CTT, what will be its mate pair read and paired end read. I am confused between the two.
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