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Question: how can I use a custom adapter sequence in trimmomatic while in Galaxy?
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gravatar for 378536209
23 months ago by
378536209 • 0
378536209 • 0 wrote:

Hi,

I want to use a custom adapter sequences in trimmomatic. But when I upload a fasta file, the options of 'Adapter sequences to use' do not change, I also can't choose the file from the history. So is there any way can I add a custom adapter sequences file to trimmomatic?
rna-seq software error galaxy • 1.3k views
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modified 23 months ago by y.hoogstrate • 460 • written 23 months ago by 378536209 • 0
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gravatar for Jennifer Hillman Jackson
23 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try the tool Trim Galore! to specify a custom adaptor sequence. Find this option on the tool form at: Trimming reads? > User defined adapter trimming > Adapter sequence to be trimmed off. Then paste in the sequence string.

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 23 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for y.hoogstrate
23 months ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

I have had good results with cutadapt Galaxy wrapper by Lance Parsons. It is not available on usegalaxy, but available in the tool shed if you have your own galaxy instance: https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/.
ADD COMMENT • link written 23 months ago by y.hoogstrate • 460
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