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Question: Adapter trimming in basespace
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gravatar for shamsher jagat
2.5 years ago by
shamsher jagat • 590
United States
shamsher jagat • 590 wrote:

I have used NuGEN RNA-seq kit and adapter sequence. is AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (TruSeq Universal Adapter) However in base space (FASTqToolkit) closest one is True seq dual HT/LT but it is not completely matching Another option is Ht/Lt common seq of 12 bases. What should be my best choice. In base space I cannot paste my adaptor seq.

Thanks

Kanwar
general question adapter trimming • 622 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by shamsher jagat • 590
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For help with that application, it would be best to contact Illumina support. Or you can try posting to a general bioinformatics board such as https://www.biostars.org.

If you want to instead process the data in Galaxy (https://wiki.galaxyproject.org/BigPicture/Choices), there are other trimming tools available. At http://usegalaxy.org, these are in the tool group NGS: QC and manipulation. In a local or cloud Galaxy, find tools in the Tool Shed (http://usegalaxy.org/toolshed) and install for use.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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