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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: