Question: Trimmomatic paired-end mode question
0
gravatar for slin023
6 months ago by
slin0230
slin0230 wrote:

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
assembly • 296 views
ADD COMMENTlink modified 6 months ago by brian.fristensky140 • written 6 months ago by slin0230

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)

ADD REPLYlink written 6 months ago by grant.hovhannisyan2.0k
0
gravatar for brian.fristensky
6 months ago by
Canada/University of Manitoba
brian.fristensky140 wrote:

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).

ADD COMMENTlink modified 6 months ago • written 6 months ago by brian.fristensky140
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