Per base sequence quality in FastQC
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؟
• 1,757 views
•
link
updated
by
GenoMax
•
written
by
khatami.s.83 •
•
written
by
khatami.s.83 •
1 answer
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
Log in to answer this question.
More posts like this
-
Illumina reads to be processed and prepared for reference genome alignment
written by Veselina •
-
fastq file sub-sampling during per position quality score graphing
written by Anand Rao
-
Interpretation of Polygenic Risk Score
written by Lb •
-
Opinion on FastQC output for HiSeq 4000 PE sequencing run
written by quokka •
-
Leftover adapter sequences after Trimmomatic trimming?
written by annsun89 •
-
FASTQ- Reverse reads of paired end sequence worse than forward reads
written by dilawerkh4 •
-
Read trimming with BBDuk
written by seta
-
Algorithms for identification of insertion sites using split reads
written by xieshaojun0621
-
Failed FastQC Per sequence GC content of MeDIP Input sample
written by Gary
-
Bwa Soft-Clipping Pattern In Read Length Distribution Using "-Q 20" Parameter
written by toni
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