Comparing MiSeq output from different runs

[strepthroat]

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]

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.