Comparing MiSeq output from different runs

strepthroat · 06-07-2018, 08:41 AM

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

GenoMax · 06-07-2018, 10:41 AM

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.

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06-07-2018, 08:41 AM	#1
strepthroat Junior Member Location: Cambridgeshire Join Date: Apr 2017 Posts: 2	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

06-07-2018, 10:41 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	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.