Hello everyone,
recently, I've been looking at two coverage plots from the same human material sequenced two times at (on average) 8x (run1) and at 30x (run2) sequence depth. I noticed (only by eye) a significant difference in the read distribution leading to high peaks in run2 and a bit messy picture, while the read distribution in run1 looks very "nice" and pretty flat. Is there a problem in the data or is this a usual picture when you deal with data of very high sequencing depth (> 30x)? Is there maybe some kind of "exponential" gain on special genomic regions like gc-rich / -poor, repetetive regions etc. that getting more and more significant the higher the sequencing depth gets?
I'd be very interested in your opinions and experiences and would be very thankful for some ideas.
Cheers,
Christoph
recently, I've been looking at two coverage plots from the same human material sequenced two times at (on average) 8x (run1) and at 30x (run2) sequence depth. I noticed (only by eye) a significant difference in the read distribution leading to high peaks in run2 and a bit messy picture, while the read distribution in run1 looks very "nice" and pretty flat. Is there a problem in the data or is this a usual picture when you deal with data of very high sequencing depth (> 30x)? Is there maybe some kind of "exponential" gain on special genomic regions like gc-rich / -poor, repetetive regions etc. that getting more and more significant the higher the sequencing depth gets?
I'd be very interested in your opinions and experiences and would be very thankful for some ideas.
Cheers,
Christoph
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