Question: trimgalore on interleaved paired-end fastq files
gravatar for DiegoVeliz
13 months ago by
DiegoVeliz0 wrote:


I'm analyzing interleaved paired-end fastq files downloaded via fastq-dump. I am trying to remove adapter sequences using Trim Galore, but I am not sure whether Trim Galore is correctly detecting that the data is interleaved, because it asks for 2 fastq files.

So my question is: Can Trim Galore process interleaved paired-end fastq files? If so, how can it be accomplished?

Thanks in advance

ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by DiegoVeliz0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


De-interlace the fastq data as the first step after downloading from NCBI, then use downstream tools. This is how:

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
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