Question: trimgalore on interleaved paired-end fastq files
0
gravatar for DiegoVeliz
8 months ago by
DiegoVeliz0
Peru/Lima
DiegoVeliz0 wrote:

Hi,

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 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by DiegoVeliz0
2
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

De-interlace the fastq data as the first step after downloading from NCBI, then use downstream tools. This is how: https://galaxyproject.org/support/ncbi-sra-fastq/#interlaced-forward-and-reverse-reads

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson25k
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