TrimGalore fastq file processing

Question

[lisanne.terrie]

Hey

We would like to perform a TrimGalore to remove low quality bases, trim adaptors and fix paired-end reads, retaining unpaired reads of at least 35 bp post-trimming. As we are masterthesis student lacking any knowledge on this we have no clue what to do. We found following command: ~/bin/trim_galore_zip/trim_galore --dont_gzip -t --paired --fastqc --retain_unpaired -a AGATCCGGAAGAGC -o Can anyone help us to understand what each parameter means and where we have to define our input files? We wondered whether we need to add the command -m 35 to remove all reads shorter than 35 bp.

Thanks a lot for the help.

[Devon Ryan]

Have you read the documentation? If not, please do so and then post any remaining questions.

[lisanne.terrie]

We've read the documentation that's why we wonder whether to add the command -m 35. The command we found is one from the literature in which the command dont_gzip is clear but we dont understand the other command like -t, -- paired -- fastqc. Which one selects for the high quality bases, which one fixes paired-end reads?

Thanks a lot for the help.

[Devon Ryan]

All of the options are described both on the command line and in the documentation that I linked to. --length specifies the minimum length for reads to keep. You probably want to tweak -q.

[lisanne.terrie]

Thank you for the documentation. We were just wondering were we need to define the input files and what you ment with 'tweak -q'.

Thank for you help.