Question: Per base sequence quality in FastQC
gravatar for khatami.s.83
18 months ago by
khatami.s.830 wrote:

The attached graphs are the result of WES (paired end reads) Quality assessment with FASTQC. Sequencing was performed by the Illumina hiseq 4000. What is the reason for the difference in quality paired end reads؟

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next-gen • 742 views
ADD COMMENTlink modified 17 months ago by genomax80k • written 18 months ago by khatami.s.830

there is no "attached graphs "

please, comment or validate (green mark on the left) all your previous questions: question about mtDNA graph coverage ; interpretation if fastqc ; Meaning of Per sequence quality scores in FastQC

ADD REPLYlink written 18 months ago by Pierre Lindenbaum127k
gravatar for genomax
17 months ago by
United States
genomax80k wrote:

This is a normal observation. Q-scores show a relative drop on R2 (specially towards the end of reads).

Possible reasons:

  • Reagents sit at 6-7C for duration of run and may show some degradation
  • Clusters start getting fatter over time and software starts having difficulty telling clusters apart
ADD COMMENTlink written 17 months ago by genomax80k
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