Region mapped by reads in only one orientation

[bioinfosm]

I cannot recollect what name these regions are referred by?

So, I see these regions along the reference, which have a lot of tiled reads mapped across them, but only in one orientation. How can one best interpret that. From various reading, I feel that reads mapping in both directions makes for more confident mapping and SNP calling.

sm

[colindaven]

Strange. I haven t seen that before. I would prefer to have reads mapped in both orientations too, but if you have a high enough coverage and there aren t too many errors towards the low quality end of the reads then things should work out ok.
Have you looked what has happened to the reads with reverse orientation just using grep etc ?

Colin

[bioinfosm]

I think towards the end-points of your fragment or LR-PCR products, one is bound to get reads mapped in one orientation, because a 36/50 mer would not start in between (because of not being 'randomly' fragmented at the end points)

Fragment & reads
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