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Old 05-12-2011, 06:51 AM   #1
vjimenez
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Default Can GAIIx introduce a bias in coverage A on T?

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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Old 05-13-2011, 04:56 AM   #2
tonybolger
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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?
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.

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?

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Old 05-13-2011, 10:54 AM   #3
vjimenez
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The gap between A and T is between 1% to 4% at the end of the sequence. But always in genomic apliaciones of eukaryotes.
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Old 05-18-2011, 04:11 AM   #4
tonybolger
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The gap between A and T is between 1% to 4% at the end of the sequence. But always in genomic apliaciones of eukaryotes.
Probably nothing too serious - how's the quality at that end?

I guess if you're only seeing it in genomic data, it could be related to the specific adapters used.
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