Hi,
I thought there was some discussion, but could not find it - regarding the data output from a chipSEQ run using the Solexa GA.
There is very little dna to work with, is what the sequencing team says. But after a run through the solexa pipeline, I see under 20% passing-filter reads aligning to the reference genome. That is way too low, and that too with error rate of about 5% !
Are there any changes or workarounds as to what might be causing it? or its simply blame it on the data! The number of clusters, % pass, intensities all look fine..
I thought there was some discussion, but could not find it - regarding the data output from a chipSEQ run using the Solexa GA.
There is very little dna to work with, is what the sequencing team says. But after a run through the solexa pipeline, I see under 20% passing-filter reads aligning to the reference genome. That is way too low, and that too with error rate of about 5% !
Are there any changes or workarounds as to what might be causing it? or its simply blame it on the data! The number of clusters, % pass, intensities all look fine..
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