Question: How To Trim Sequences With Low Quality Scores
gravatar for Hoang, Thanh
5.5 years ago by
Hoang, Thanh200
Hoang, Thanh200 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:"" tool_runner?tool_id="fastq_quality_t" rimmer=""> but am not sure if this is the right tool to use and how to use the parameter settings? Best regards Thanh
ADD COMMENTlink modified 5.4 years ago by Jennifer Hillman Jackson25k • written 5.5 years ago by Hoang, Thanh200
gravatar for Jennifer Hillman Jackson
5.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Hillman-Jackson Galaxy Support and Training
ADD COMMENTlink written 5.4 years ago by Jennifer Hillman Jackson25k
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