Question: Trim Galore Bug?
gravatar for datascientist28
4.4 years ago by
University of Washington
datascientist28470 wrote:

I'm having some trouble with my output files after I use trim galore. I think I might have found the issue but I'm curious if anyone has had a similar problem. The command I give trim galore specifies paired end mode but for some reason cut adapt is trimming in single end mode. Anyone know if this is a bug or am I thinking about this wrong?

Below is my trim_galore report . I highlighted in bold my what I mean...


Input filename: Regeneration_ATAC_1hpa-1_R1.fastq.gz

Trimming mode: paired-end

Trim Galore version: 0.4.1

Cutadapt version: 1.10

Quality Phred score cutoff: 20

Quality encoding type selected: ASCII+33

Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; user defined)

Maximum trimming error rate: 0.1 (default)

Minimum required adapter overlap (stringency): 1 bp

Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1

Running FastQC on the data once trimming has completed

Output file will be GZIP compressed


This is cutadapt 1.10 with Python 2.7.11

Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA Regeneration_ATAC_1hpa-1_R1.fastq.gz

Trimming 1 adapter with at most 10.0% errors in single-end mode ...

Finished in 1463.06 s (25 us/read; 2.45 M reads/minute).

paired end trim galore • 3.8k views
ADD COMMENTlink modified 4.4 years ago by dariober11k • written 4.4 years ago by datascientist28470

Can you post the full command line? Based on the log above it appears that you only have one fastq file.

ADD REPLYlink written 4.4 years ago by genomax92k
trim_galore --paired --phred33 --fastqc --nextera --trim1 Regeneration_ATAC_1hpa-1_R1.fastq.gz Regeneration_ATAC_1hpa-1_R2.fastq.gz
ADD REPLYlink modified 4.4 years ago by genomax92k • written 4.4 years ago by datascientist28470

I am not a trim galore user but looking at the manual it does not appear that --paired option is used unless you also specify --length option.

--paired This option performs length trimming of quality/adapter/RRBS trimmed reads for paired-end files. To pass the validation test, both sequences of a sequence pair are
required to have a certain minimum length which is governed by the option --length (see above).

ADD REPLYlink written 4.4 years ago by genomax92k

I think it's supposed to be --trim-1, not --trim1.

ADD REPLYlink written 4.4 years ago by igor11k

I have the same issue, does anyone have any idea what is going on?

ADD REPLYlink written 4.2 years ago by ofonov0

Read @dariber's comment. It's all fine. That's just how trim galore runs

ADD REPLYlink written 4.2 years ago by datascientist28470
gravatar for dariober
4.4 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

I think it's all fine. I think trim_galore in paired end mode runs trim_galore/cutadapt in single end mode for read 1 and read 2 independently and without discarding any read (hence the single-end log you see). Then, in a second pass, it removes read pairs where either read 1 or read 2 fail to pass the length threshold.

You might want to check with Felix, the developer, he's usually very quick and helpful answering questions.

ADD COMMENTlink written 4.4 years ago by dariober11k
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