Per base sequence quality before and after truseq adapters removal

Question

[cristianrohr768]

Hello all,

I have Illumina Truseq data from a custom design sequenced on a MiSeq. Before removal of adapters sequences, quality from position starting to 85bp (reads of 151 bp) drops dramatically. After removal of the adapters sequences, quality is really high, more than at the start of the reads, is this normal? I mean I expect data to be better, but not at this level of improvement

Answer 1

[harold.smith.tarheel]

Yes, because the low quality in later cycles is largely the result of sequencing past the adapter ends. By trimming adapters (and subsequent sequences) you remove those low-quality data.

And read quality is always lower for the first ~five cycles of sequencing; search this forum or Seqanswers for an explanation.