Hi there,

I am working on pooled sequencing samples of drosophila. I have three populations. When I first submitted my samples for (paired end) Illumina sequencing, the biotech center informed me that they messed up sequencing the third sample, and would have to redo the run. I still received the data from the other two samples which were fine. When they redid the sequencing for the thid population, I also received another set of reads from populations 1 and 2 from the second run. My advisor advised that I concatenate the fastq files from the original and redo runs for these populations to obtain more depth. I'm wondering a couple things;

1. Has anyone else done something like this with their data

2. Could this create any sort of problems or caveats that I should be aware of when analyzing my data downstream? (I'm currently using Popoolation2)

Thank you