How are mate pairs formed and stored

[ashutosh]

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.

[mastal]

See these pages from the Illumina website for explanations of mate-pair and paired-end with respect to Illumina's technology.

http://www.illumina.com/technology/mate_pair_sequencing_assay.ilmn

http://www.illumina.com/technology/paired_end_sequencing_assay.ilmn

[ashutosh]

I have already read the above links but it didn't get clear thats why I posted with an example. Can you please answer it with respect to the above genome.

[SylvainL]

DNA polymerisation is always from 5' to 3' so a read CTT will either map CTT or AAG (T is complement of A, and G of C) (reverseComplement) on the genome....

[ashutosh]

That is the just the reverse complement of the read......what are mate pairs is not clear to me??

[jwag]

Mate-pair refers to the way the sample was prepared, but are sequenced the same way as regular paired end libraries. Regular PE reads are outside in (L>====<R) but because of the way mate-pair libraries are prepared, MP sequences are actually inside out (L<====>R) because of the circularization step.