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Using FASTQ Groomer and Clip to remove adapter sequences from RNA-Seq data in Galaxy

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In this video step, we will use the FASTQ Groomer and Clip tools to strip adapter sequences from raw RNA-Seq data in Galaxy.

We begin with the results of a FastQC job in Galaxy.

Click on the link "Overrepresented sequences" under the report summary. Highlight and copy the most over-represented sequence — the first one listed.

In the toolbar, choose "FASTQ Groomer" under "NGS: QC and manipulation".

Make sure the file listed under "File to groom" is the one used in the FASTQC report, here "RNA-Seq.fastq". Click "Execute".

This tool converts the FASTQ file into a more Galaxy-friendly format.

Once the job has finished load the "Clip" tool also under "NGS: QC and manipulation".

Set the "Source" parameter to "Enter custom sequence" and paste the previously copied RNA sequence into the "custom clipping sequence" text box.

In this example we want to keep both clipped and unclipped sequences so change the "Output options" parameter accordingly; click "Execute".