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Question: Analysing paired end RNAseq data with poor quality score
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gravatar for fong.pooihar
4.2 years ago by
fong.pooihar • 0
Malaysia
fong.pooihar • 0 wrote:

Hello,

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.  

Regards

Fong

Per base quality graph
assembly tophat alignment galaxy rna-seq • 1.9k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by fong.pooihar • 0
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gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The quality scaling looks off and you want to process the two ends as distinct datasets. Try this method as a start.
http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

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 COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 4.2 years ago by fong.pooihar • 0
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