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Old 11-08-2008, 02:58 AM   #1
yamayaya
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Default GC content

It seems that solexa prefer to sequencing higher GC content region. Does anybody face to this problem?
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Old 11-08-2008, 06:08 AM   #2
kopi-o
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Yes, we have run into this phenomenon. It is also mentioned here: Dohm et al., Substantial biases in ultra-short read data sets from
high-throughput DNA sequencing, Nucleic Acids Research, 2008, 110
(doi:10.1093/nar/gkn425)
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Old 11-08-2008, 06:34 AM   #3
yamayaya
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Thanks. I also have read that paper, but they deal with beta genome etc.
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Old 02-24-2009, 01:05 PM   #4
bioinfosm
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Any thoughts on GC content bias on the depth of coverage? I would like to see evened-out depth of coverage by taking GC-content into account; but it doesnt look even from the R linear model linearization I tried!
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Old 02-25-2009, 12:30 AM   #5
huguesparri
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Are you sure it doesn't come from the library preparation?
If you read this article:
http://www.nature.com/nmeth/journal/...meth.1270.html
you'll see that in the last purification step, when you extract your PCR from the gel, you can improve A-T rich sequence representation by melting agarose at room temperature...

Did you try to compare a RT melted sample and a 50 melted sample?
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