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Question: clip adapter sequences
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gravatar for tali.mandel
4.0 years ago by
tali.mandel • 10
Hebrew University
tali.mandel • 10 wrote:

Hello,

I am trying to clip adapter sequences from fastq files, however when I open this tool it doesnt identify my fastq files in the "library to clip" window.

Any idea to help me?

Thanks

Tali
galaxy chip-seq • 1.2k views
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modified 4.0 years ago • written 4.0 years ago by tali.mandel • 10
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gravatar for mokona__modoki
4.0 years ago by
mokona__modoki • 10
France
mokona__modoki • 10 wrote:

Hello

Did you check the format of the fastq file ? You have different quality encodings for fastq files... Try grooming your fastq file. I've had such problems and grooming usually did the trick.

By the way generaly the data you want to clip is fastq but the adapter sequences should be in a .fasta file. That's how I did it and it worked.

Hope it helps

 
ADD COMMENT • link modified 4.0 years ago • written 4.0 years ago by mokona__modoki • 10
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gravatar for tali.mandel
4.0 years ago by
tali.mandel • 10
Hebrew University
tali.mandel • 10 wrote:

Thanks

I worked perfectly!

 

Tali

 
ADD COMMENT • link written 4.0 years ago by tali.mandel • 10
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