Closed unikill066 closed 2 months ago
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.
_val_
extension is always added as a matter of course, you can use a single command afterwards to batch rename files afterwards. 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.
Just to confirm, there is no flag to not add the val, so rename s/_val_/_/
will have to do. All the best!
I usually have paired-end sequencing data, and I intend to run
trim_galore
on the example files below:I am attempting to execute
trim_galore
on all these samples using the following commands: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.