Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: trimgalore on interleaved paired-end fastq files
0
gravatar for DiegoVeliz
13 months ago by
DiegoVeliz • 0
Peru/Lima
DiegoVeliz • 0 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
fastq interleaved trim galore paired-end • 695 views
ADD COMMENT • link •
modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by DiegoVeliz • 0
2
gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour