trimming paired end reads using Trim galore

Hedi86 · 06-26-2018, 09:38 AM

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

fkrueger · 06-29-2018, 01:27 AM

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.

Hedi86 · 12-18-2018, 08:34 AM

thank you for your replay

for downstream analyses in Bismark i used both Val-trimmed-R1 and Val-trimmed-R2 files (because libraries prepared using NuGEN kit). however, bismark produced only one BAM file with R1 extension name. is it normal for pair end alignment?

Best

fkrueger · 12-18-2018, 08:35 AM

Yes, this is normal. Paired-end BAM files have Read 1 and Read 2 on consecutive lines, so there is only one file per read pair.

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06-26-2018, 09:38 AM	#1
Hedi86 Member Location: Norway Join Date: Oct 2017 Posts: 16	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

06-29-2018, 01:27 AM	#2
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 614	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.

12-18-2018, 08:34 AM	#3
Hedi86 Member Location: Norway Join Date: Oct 2017 Posts: 16	thank you for your replay for downstream analyses in Bismark i used both Val-trimmed-R1 and Val-trimmed-R2 files (because libraries prepared using NuGEN kit). however, bismark produced only one BAM file with R1 extension name. is it normal for pair end alignment? Best

12-18-2018, 08:35 AM	#4
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 614	Yes, this is normal. Paired-end BAM files have Read 1 and Read 2 on consecutive lines, so there is only one file per read pair.