Question: Analysing paired end RNAseq data with poor quality score
gravatar for fong.pooihar
3.8 years ago by
fong.pooihar0 wrote:


I'm new in NGS and i'm currently working on RNA-seq. I had 6G of illumina reads and proceed with the data processing. After joining my paired end reads into a single file, I ran FastQC to get the median quality score before trimming the reads. But i found out the scores of my reads are very bad. I would like to know, should I continue to trim my reads by using 2 as the median quality score or map my reads without trimming them? the following image is the box plot for the quality scores across all bases of my data.

Any constructive advice/comments are highly appreciated. Thanks.  



Per base quality graph

ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by fong.pooihar0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The quality scaling looks off and you want to process the two ends as distinct datasets. Try this method as a start.

You will want to run FastQC on the original data, likely Groom, then run FastQC again to see if any quality trimming is needed. The tools are in the group "NGS: QC and manipulation".

Best, Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k

Thanks for your suggestion, i will try it out and see how it goes. 

ADD REPLYlink written 3.8 years ago by fong.pooihar0
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