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Question: Clip
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gravatar for William Yarosh
5.3 years ago by
William Yarosh • 10
William Yarosh • 10 wrote:
Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use this program so it will clip the 5' end or a way to make all my reads the reverse complement and run it through this program? Thanks
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modified 5.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.3 years ago by William Yarosh • 10
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gravatar for Jennifer Hillman Jackson
5.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, The "Clip" program only acts on the 3' end. In some cases, running "FastQC" to isolate adapter regions, then using a tool like "FASTQ Trimmer" or "Trim" will work (if the lengths are somewhat fixed). Alternately, the tools "NGS: QC and manipulation -> Reverse-Complement or Manipulate FASTQ" will reverse compliment reads. For the second, the option is located in Manipulate Reads -> Manipulate on 'Sequence Content' -> Sequence Manipulation Type:. There are several options here, including trim again, but also "Reverse Complement". Hopefully this helps! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.3 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
5.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello, This Galaxy wrapper is based on the FASTX-Toolkit tool by the same name. A link to the original is at the bottom of the tool's form in the UI. To see the Galaxy wrapper, it is in the source here: galaxy-central / tools / fastx_toolkit https://bitbucket.org/galaxy/galaxy-central Questions about the core tool can be directed to the tool author. Help with running a local Galaxy or tools in general is on the galaxy-dev@bx.psu.edu mailing list: http://wiki.galaxyproject.org/Support#Mailing_Lists If you create a new wrapper with more options, please consider contributing it to the Tool Shed, as this tool is super popular and the option for 5' clipping has come up before. http://wiki.galaxyproject.org/Tool%20Shed Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.3 years ago by Jennifer Hillman Jackson ♦ 25k
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