I have very low cluster passing filter for my SELEX pool Sequencing in Miseq using Nextera Miseq reagent kit V2 (300 cycles) and XT index kit set B. I performed all QC of pools after Adaptor and Index PCR. What could be the reason or is it normal for Aptamer sequencing which is really short (Library length is 84 and after index PCR , the length is 205).

Looking forward for your kind help.