Trimmomatic paired-end mode question

Question

[slin023]

Hi, I have trimmomatic 0.39-1 installed via bioconda and I have read the manual. I am confused about giving input files for "paired-end" mode in trimmomatic command lines. I followed up the script and revised it.

java -jar /opt/anaconda3/pkgs/trimmomatic-0.39-1/share/trimmomatic-0.39-1/trimmomatic.jar -threads 16 -phred33 ${SRR}_1.fastq.gz ${SRR}_2.fastq.gz ${SRR}_1_paired.fastq.gz ${SRR}_1_unpaired.fastq.gz ${SRR}_2_paired.fastq.gz ${SRR}_2_unpaired.fastq.gz ILLUMINACLIP:/opt/anaconda3/pkgs/trimmomatic-0.39-1/share/trimmomatic-0.39-1/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

so for example, if I would like to put raw read data 00_fastq.text, I change ${SRR}_1.fastq.gz into /Users/maysonlin/Downloads/PhormiaMaleFemaleTranscriptome_Stranded/Phormia raw data/00_fastq/00_1.fastq.qz, do I follow the right track?

I tried to revise the directory and file names, it gives this

Usage: PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>... or: SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>... or: -version

[grant.hovhannisyan]

which exact command have you tried running? did it throw any error? what you propose seems correct, instead of ${SRR}_1.fastq.gz, you just need to locate you own file. You also have to specify the reverse reads, and 4 output files (forward paired, forward unpaired, reverse paired, reverse unpaired)

Answer 1

[brian.fristensky]

You didn't include the PE option to tell trimmomatic that you are giving it two paired end files.

I put the PE option into your command line:

java -jar /opt/anaconda3/pkgs/trimmomatic-0.39-1/share/trimmomatic-0.39-1/trimmomatic.jar PE -threads 16 -phred33  ${SRR}_1.fastq.gz ${SRR}_2.fastq.gz ${SRR}_1_paired.fastq.gz ${SRR}_1_unpaired.fastq.gz ${SRR}_2_paired.fastq.gz ${SRR}_2_unpaired.fastq.gz ILLUMINACLIP:/opt/anaconda3/pkgs/trimmomatic-0.39-1/share/trimmomatic-0.39-1/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

You can avoid these kinds of picky errors by using the BIRCH system. BIRCH has an application called blreads that unifies the steps in NGS genome or transcriptome assembly in an intuitive point and click application. See the web tutorials on Genome Assembly or Transcriptome assembly, which include read trimming.

You can see blreads in action in the YouTube video BIRCH Desktop Bioinformatics (long version).