The --nextseq argument doesn't change the parameters of cutadapt

[josephhughes]

I'm using the following command in trim_galore:

trim_galore --nextseq 20 --dont_gzip --length 50 --paired $fq1 $fq2

and I was expecting this to be reflected in the trim_report.txt with -nextseq-trim=3'CUTOFF but I just get:

-j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC

which is the same as when I specify the following in trim_galore:

trim_galore -q 20 --dont_gzip --length 50 --paired $fq1 $fq2

Have I misunderstood what --nextseq does or am I mis-specifying something?

[FelixKrueger]

This is very odd, I have just run a few tests with and w/o --dont_gzip, and I consistently get:

trim_galore --dont --paired --length 50 test_R1.fastq test_R2.fastq

>>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file test_R1.fastq <<<
This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG test_R1.fastq

or

trim_galore --dont --nextseq 20 --paired --length 50 test_R1.fastq test_R2.fastq`

>>> Now performing quality (cutoff '--nextseq-trim=20') and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file test_R1.fastq <<<
This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j 1 -e 0.1 --nextseq-trim=20 -O 1 -a TGGAATTCTCGG test_R1.fastq

Which version of Trim Galore are you using?

[josephhughes]

Really sorry. My Friday mistake :(.

[FelixKrueger]

No worries, glad it got resolved! Have a good weekend!