For my research project we are trying to under why the full adapter sequences were provided for paired end adapter trimming (adapters/NexteraPE-PE.fa) instead of partial the adapter sequences (i.e. CTGTCTCTTATACACATCT+AGATGTGTATAAGAGACAG) as recommended by Illumina. Indeed 2% more reads are trimmed using adapters/NexteraPE-PE.fa file.
For my research project we are trying to under why the full adapter sequences were provided for paired end adapter trimming (adapters/NexteraPE-PE.fa) instead of partial the adapter sequences (i.e. CTGTCTCTTATACACATCT+AGATGTGTATAAGAGACAG) as recommended by Illumina. Indeed 2% more reads are trimmed using adapters/NexteraPE-PE.fa file.