Question: how can I use a custom adapter sequence in trimmomatic while in Galaxy?
0
gravatar for 378536209
17 months ago by
3785362090
3785362090 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 • 899 views
ADD COMMENTlink modified 17 months ago by y.hoogstrate460 • written 17 months ago by 3785362090
1
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k
1
gravatar for y.hoogstrate
17 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 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 COMMENTlink written 17 months ago by y.hoogstrate460
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