I have 13 samples which were initially sequenced and expected to yield around 30 million reads per sample, however we only managed to get half of that. Therefore we re-pooled the samples and ran them again, getting more reads this time. Therefore I have 2 files per sample, run 1 (with low reads) and run 2 (with high reads). I tried merging these files together (using cat function) to get even greater depth but my QC analysis shows a lot of duplications. Is there a better way of merging these files whilst avoiding high levels of duplications? Thanks!