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

Join Date: Oct 2017
Posts: 13
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
Hedi86 is offline   Reply With Quote
Old 06-29-2018, 01:27 AM   #2
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Location: Cambridge, UK

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Posts: 611

Hi Hedi86,

for RRBS the command would be:

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,

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.
fkrueger is offline   Reply With Quote

illumina, paired end read, rrbs, trim galore

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