Trimming with Rockhopper

Question

[elhenawy]

Hi all, I am trying to analyze my bacteria transcriptomes with Rockhopper. Do I need to trim illumina adaptors beforehand? I tried to find if this is a build-in function in Rockhopper, but couldn't tell. Thanks!

[ATpoint]

As always with new fastq files, use fastqc to see if adapter contamination is an issue. If not, don't do it.

[elhenawy]

Thank you! That makes sense!

Answer 1

[GenoMax]

There should be no harm in scanning/trimming your data before feeding it to rockhopper. User guide for rockhopper does not seem to mention adapters.

[Kevin Blighe]

Indeed, last time that I used Rockhopper, I performed trimming with Trim Galore!

export PATH="/Programs/cutadapt-1.8.3/bin:$PATH"
trim_galore --qual 30 --gzip --length 75 --illumina --paired R1.fastq.gz R2.fastq.gz --output_dir out/ --fastqc

Note that this also runs FASTQC, recommended by ATpoint

[elhenawy]

Thanks a lot! This helps!