I have a graphic that show an increase in coverge of A over T, and It increses until the end sequence, in all lanes of paired ends runs of 72 pb. Can GAIIx introduce a bias in coverage A on T?
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Yes, for some reason, our recent datasets seem to favour A over T and G over C, when the quality is a bit crappy. We see a rise in N calls roughly correlating this discrepancy.Originally posted by vjimenez View Post
An older dataset (of lower quality) of our is different, with C considerably over G, and T slightly over A.
I don't know if this is an effect from the base-caller or if it's from the adapter sequences, but it's there, around 1% difference. How much of a gap are you seeing?Last edited by tonybolger; 05-18-2011, 04:09 AM. -
The gap between A and T is between 1% to 4% at the end of the sequence. But always in genomic apliaciones of eukaryotes.Veronica Jimenez Jacinto
UUSM.Comment
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Probably nothing too serious - how's the quality at that end?Originally posted by vjimenez View Post
I guess if you're only seeing it in genomic data, it could be related to the specific adapters used.Comment
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