Good day colleagues. I have running some RNA-seqs on the illumina miseq with a control and two test groups. I have 3 samples of each group. I did one miseq chip with all 9 samples on, then did another two miseq chips with 5 samples on one then 4 on the other (to increase amount of data).
I have analysed the data all good. My boss however is unhappy that the data has come from different miseq runs on separate days. They want me to merge the fastq files from the different runs into one fastq files for each sample. This is in order that it looks better to reviewers when it comes to publishing time.
I feel this is a] a bit pointless b] like it might it fudging the data. I also couldnt merge the fastq files successfully using the cat function.
Does anyone know a way to either successfully blend fastq files or have a solid explanation as to why it will make no difference (so i can just tell him it wont work and we can all move on).