Question: How To Trim Sequences With Low Quality Scores
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gravatar for Hoang, Thanh
4.6 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: main.g2.bx.psu.edu="" 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
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ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson23k • written 4.6 years ago by Hoang, Thanh200
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gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson23k 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 http://galaxyproject.org
ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson23k
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