This may not be related to bioinformatics, but I demultiplexed one illumina sequence run and noticed that one sample has quite different the # of reads from different lanes. (used the same index sequence in the samplesheet)
sample1 from lane1,3,4 : 0 reads
sample1 from lane2 : 8 million reads.
Would you mind explaining why it happened? It's nanostring sequence data. If you need more info about the libraries, I will definitely ask questions to my coworkers who prepared the libraries and ran the sequencer.