Low quality bases at the starts of HiSeq 2 x 100bp reads

Question

[Louis Kok]

Hi all, I wonder if anyone of you has problem that the base quality is low (<Q20) at the start (left end) of the sequence reads generated from 2 x100bp pair-ended sequencing, and increase after around 10 bases? I know that quality drops at the right end but this is the first time I saw low base quality at the left end. Any reason behind it? Thanks in advance.

Answer 1

[Biogeek]

Hexamer primer bias from the start of the reaction? Quite common at the 5'. I'd recommend cropping the first 10 reads then applying at least Q20 to your reads.

What program are you using for QC and cleaning of the reads?

[Louis Kok]

Hi. Thanks for the explanation. I use fastqc to quality checking and use trim_fastq.pl for trimming. Alternatively, I use prinseq for trimming at both ends sometimes.

[Louis Kok]

I found out that this happens in Illumina transcriptome sequencing. Does this happen in amplicon sequencing as well?

[User 59]

Amplicons can have low diversity, which can decrease the quality of runs substantially.