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Old 06-26-2018, 09:38 AM   #1
Hedi86
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Location: Norway

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Default trimming paired end reads using Trim galore

Dear all

im trying to trim paired-end RRBS illumina reads using Trim galore. as far as i understood, paired end reads must be trimmed using --paired option following by file names. i tried : trim_galore --paired r1.fastq.gz r2.fastq.gz. however at the end, im getting only trimmed file for read 1 and nothing for read 2. any idea why?

thank you so much in advance
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Old 06-29-2018, 01:27 AM   #2
fkrueger
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Hi Hedi86,

for RRBS the command would be:

Code:
trim_galore --rrbs --paired r1.fastq.gz r2.fastq.gz
Which version of Trim Galore were you using (the latest one is v0.5.0, https://github.com/FelixKrueger/TrimGalore/releases).

Trim Galore will trim R1 first, R2 second, and then perform a validation step which p0roduces 2 new files that contain _val_ in their file names (for validated). Once this is done, the files called _trimmed_ ... are being deleted. If there are any error messages on the screen they might help identify where the problem lies.
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illumina, paired end read, rrbs, trim galore

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