Dear all, I´m new with small RNA sequencing data. I just have a problem, I have 96 sampes of three different conditions. They have been prepared with smallRNA Truseq library (Illumina) and sequenced with V3 chemistry in 4 different pools in 4 lanes (HISeq 2500) in order to get around 10 millions of reads from each sample. After sequencing, one of the pools (24 samples) yielded less reads than expected (sometimes less than a half than the others, around 5 M). These samples were resequenced but still, similar reads were obtained and core facility tell me to merge the reads with the previous ones. However, I´m not sure about this... My question is that since I´m looking also for new/rare miRNAs, wich are usually in low frequency, I cannot detect them with a 2 x 5 million reads, instead of 10 M in one run, right? Additionally, the 24 samples with this problem belongs to one condition in my experiment, therefore now I cannot compare to the other two conditions ? I really appreciate your comments, thanks!!