Hello,

The drop in quality score is in the middle of the read - you wouldn't want to trim these sequences and lose the rest of the sequence data 3' or 5'. FastQC also gave it a "pass" (that is the green checkmark, you would see a yellow "!" or red "x" if the tool thought there was a quality issue).


For trimming in general, the tool " FASTQ Trimmer" is a simple option that can be used along with the results from FastQC. Say for instance, the first 5' 6 bases had low quality across the dataset, this tool could easily remove that data.

Hopefully this helps,

Jen
Galaxy team

On 6/18/13 11:59 AM, Hoang, Thanh wrote:
Hi guys,
I did quality control on my RNA-seq data using FastQC. In the report for Per base sequence quality, there are some base positions with the quality scores less than 20 ( see attached picture) . I am just wondering if there is any way to remove these? I looked at the FASTQ Quality Trimmer <https://main.g2.bx.psu.edu/tool_runner?tool_id=fastq_quality_trimmer> but am not sure if this is the right tool to use and how to use the parameter settings?
Best regards
Thanh


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