Hello everyone,
I am entering the world of genomics service providers and I love it. My group relies a lot on the SAV files to check the data, followed by the classic QC pipeline that includes demux, FastQC, MultiQC and FASTQCscreen. There are a few bits and bobs of the SAV data that I don't necessarily understand and I was hoping that someone here may help.
1) The top and bottom surfaces of a flow cell. I know that the flow cells do not get imaged from top and bottom as they are positioned on a dark support. Therefore, the image can only come from the top, I am assuming. Also, the sample library and the reagents are only pumped through the flow cell. I do not understand what is the purpose of the image of the intensities of the "bottom" surface of the flow cell. What do they mean exactly with top and bottom? Why would we be interested in having both?
2) For example in a MiSeq run, in the summary of the data, we get the data for Read 1 (ok), Read 2 (?), Read 3 (?) and Read 4 (ok). I understand that under the reads 1 and 4 we can find the metrics for the forward and reverse reads if paired end sequencing, but what is Read 2 and Read 3?
Thanks to whoever will reply,
G.
I am entering the world of genomics service providers and I love it. My group relies a lot on the SAV files to check the data, followed by the classic QC pipeline that includes demux, FastQC, MultiQC and FASTQCscreen. There are a few bits and bobs of the SAV data that I don't necessarily understand and I was hoping that someone here may help.
1) The top and bottom surfaces of a flow cell. I know that the flow cells do not get imaged from top and bottom as they are positioned on a dark support. Therefore, the image can only come from the top, I am assuming. Also, the sample library and the reagents are only pumped through the flow cell. I do not understand what is the purpose of the image of the intensities of the "bottom" surface of the flow cell. What do they mean exactly with top and bottom? Why would we be interested in having both?
2) For example in a MiSeq run, in the summary of the data, we get the data for Read 1 (ok), Read 2 (?), Read 3 (?) and Read 4 (ok). I understand that under the reads 1 and 4 we can find the metrics for the forward and reverse reads if paired end sequencing, but what is Read 2 and Read 3?
Thanks to whoever will reply,
G.
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