We have a problem with whole transcriptome libraries on Ion Proton. We sequence exomes from Ampliseq Exome kit  - ok, more than 300 exome sequenced for 1 year. We sequence targeted panels- ok. But we cannot sequence whole transcriptome libraries prepered by Whole Transcriptome RNAseq kit - we receive extremely low loading on Ion Proton chip -10-15% in comparison to 80-87% of exome  libraries. What is the reason? We had one ok seq run for whole transcriptome and 3 bad runs. Exomes between whole transcriptome runs were ok (enrichment and sequencing kits ok)/