It seems that solexa prefer to sequencing higher GC content region. Does anybody face to this problem?
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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, 1–10
(doi:10.1093/nar/gkn425) -
Thanks. I also have read that paper, but they deal with beta genome etc.Comment
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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!--
bioinfosmComment
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Are you sure it doesn't come from the library preparation?
If you read this article:
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?Comment
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