Advantages/Disadvantages of reads mapping on Different contigs?
Dear all,
i want to know the advantages/ Disadvantages of Read/Mate mapping on Same and on Different contigs.
for exemple: Contigs Range are:
contig1: 1000-4000; contig2: 4500-5500 contig3: 6000-7000 contig4: 8000-10000
On Same Contig
ReadA 35 abc 1942 37 51M = 4038 97
ReadAMate 177 abc 4038 37 51M = 1942 -97
On Different Contig
ReadC 113 abc 1748 25 51M = 6525 4777
ReadCMate 35 abc 6525 25 51M = 1748 -4777
Anyone can help?
Thanks in advance
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If you know the relative position of the contigs then why don't you make a supercontig and use that for mapping?
Obviously i'll make scaffold from this data :) but i want to know the reason of read/mate mapping on same contig and on different contig. and its significance from biological point of view.
The mates on different contigs are evidence of ordering and distance (or rearrangements/repeats).