I have recently received data from a RNA-Seq experiment. Apparently there has been a drop in the cluster density and samples had to be repeated in order to achieve the minimum number of reads and for that reason I have received two fastq files from two different lanes per sample. When I analyse the fastq files, both have a similar number of reads (15m).
Hiow should I proceed with the analysis of these files? Should I analyse them individually? Should I combine them some how? Any ideas will be greatly appreciated
Thanks in advance and kind regards