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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