Queries regarding TrimGalore

[unikill066]

I usually have paired-end sequencing data, and I intend to run trim_galore on the example files below:

121_1_L001_R1_001.fastq.gz
121_2_L001_R1_001.fastq.gz
121_3_L001_R1_001.fastq.gz
121_4_L001_R1_001.fastq.gz
121_1_L001_R2_001.fastq.gz
121_2_L001_R2_001.fastq.gz
121_3_L001_R2_001.fastq.gz
121_4_L001_R2_001.fastq.gz

I am attempting to execute trim_galore on all these samples using the following commands:

trim_galore --paired --cores 4 121_1_L001_R1_001.fastq.gz 121_1_L001_R2_001.fastq.gz
trim_galore --paired --cores 4 121_2_L001_R1_001.fastq.gz 121_2_L001_R2_001.fastq.gz
trim_galore --paired --cores 4 121_3_L001_R1_001.fastq.gz 121_3_L001_R2_001.fastq.gz
trim_galore --paired --cores 4 121_4_L001_R1_001.fastq.gz 121_4_L001_R2_001.fastq.gz

Here are my queries: Is there an efficient method to run all the fastq files at once with a single command, or do I need to use a script? Additionally, when executing trim_galore, I aim to prevent the _val_1 and _val_2 prefixes from being appended to the newly generated fq.gz files.

[FelixKrueger]

I am sure there is some command line magic that would allow you to run things more efficiently, you should be able to find solutions by some googling or asking ChatGPT.

Here are a few thoughts:

• are your samples biological 4 replicates of the same sample/condition, or are they 4 technical replicates? In the latter case, you might want to merge all R1 and all R2 files, and then only use a single trimming command.

• in case you need to run these 4 jobs, some bash scripting might also achieve the same results. Here is a slight modification of something I have run in the past:

  ls | sed s/R._001.fastq.gz$// | sort | uniq | xargs -P4 -I PREFIX bash -c 'trim_galore --paired --cores 4  PREFIXR1* PREFIXR2*'

This command should run 4 processes in parallel. The piped string (unique portion of the filename) is used as PREFIX, and is substituted whenever it is seen in the following command. Using another instance of bash -c to allow * expansion.

• the _val_ extension is always added as a matter of course, you can use a single command afterwards to batch rename files afterwards.

[unikill066]

Thank you, @FelixKrueger. I wonder if there is a flag available for not adding any extensions such as _val_. However, if there isn't, that's fine—I can rename then files accordingly.

[FelixKrueger]

Just to confirm, there is no flag to not add the val, so rename s/_val_/_/ will have to do. All the best!