Changes

== Diagnose sequencing quality ==

== Diagnose sequencing quality ==

Qplot is designed and implemented by the need of checking sequencing quality.  

Qplot is designed and implemented by the need of checking sequencing quality.  

Besides the exampled of analyzing RNA-seq data as in the manuscript,  

Besides the exampled of analyzing RNA-seq data as in the manuscript,  

here we demonstrate two scenarios in which qplot help us identify potential problem after obtaining sequencing data.  

here we demonstrate two scenarios in which qplot help us identify potential problem after obtaining sequencing data.  

* Base quality distributed abnormally

* Base quality distributed abnormally

Further we notice that effects is caused by different software from Illumina sequencers.  

Further we notice that effects is caused by different software from Illumina sequencers.  

In this particular example, all base qualities are wrongly added '33'. Such data used in variant calling may increase false positive SNP calling.

In this particular example, all base qualities are wrongly added '33'. Such data used in variant calling may increase false positive SNP calling.

* Bar-coded samples

* Bar-coded samples