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Old 06-07-2018, 08:41 AM   #1
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Location: Cambridgeshire

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Default Comparing MiSeq output from different runs

Hi, I have about 4 different MiSeq runs i have data for. I have pipelined the fastq files through bowtie-samtools-cuffdiff to compare cDNA libraries of different samples. A thought that just occured to me is some of the times i loaded a 15pM library and sometimes i loaded a 8pM library into the MiSeq cartridge (150bp v3) .

Does anyone know if its still possible to combine the data. Does the data get normalized against total number of reads?

Thanks, Will
strepthroat is offline   Reply With Quote
Old 06-07-2018, 10:41 AM   #2
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If you are using DESeq2/edgeR then they will account for differences in the total number of reads. You could downsample the data to similar levels as an option.
GenoMax is offline   Reply With Quote

bowtie, cuffdiff, loading concentration, miseq, rna seq

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