Can GAIIx introduce a bias in coverage A on T?

vjimenez · 05-12-2011, 07:51 AM

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?

tonybolger · 05-13-2011, 05:56 AM

Quote:

Originally Posted by vjimenez

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?

vjimenez · 05-13-2011, 11:54 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.

tonybolger · 05-18-2011, 05:11 AM

Quote:

Originally Posted by vjimenez

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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05-12-2011, 07:51 AM	#1
vjimenez Junior Member Location: Cuernavaca, Morelos, Mexico Join Date: Oct 2009 Posts: 4	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? __________________ Veronica Jimenez Jacinto UUSM. Last edited by vjimenez; 05-12-2011 at 07:55 AM.

05-13-2011, 11:54 AM	#3
vjimenez Junior Member Location: Cuernavaca, Morelos, Mexico Join Date: Oct 2009 Posts: 4	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.