Using trimmomatic on multiple paired-end read files

[shashankgupta]

I need help to write a for loop to run Trimmomatic tool for quality trimming of paired end fastq files.
I need to write a for loop so that I can run an executable for all multiple files.

Input PE files looks like - C1_S1_L001_R1_001.fastq.gz
C1_S1_L001_R2_001.fastq.gz

C2_S39_L001_R1_001.fastq.gz
C2_S39_L001_R2_001.fastq.gz

T2_S41_L001_R1_001.fastq.gz
T2_S41_L001_R2_001.fastq.gz

T6_S45_L001_R1_001.fastq.gz
T6_S45_L001_R2_001.fastq.gz

To run trimmomatic for the paired reads corresponding to C1_S1_L001_R1_001.fastq.gz and C1_S1_L001_R2_001.fastq.gz, the following command works:

java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 C1_S1_L001_R1_001.fastq.gz C1_S1_L001_R2_001.fastq.gz C1_R1_paired.fq.gz C1_R1_unpaired.fq.gz C1_R2_paired.fq.gz C1_R2_unpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35

The framework provided by trimmomatic

java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] <input 1> <input 2> <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...

Any help please!
Thanks!

[wdecoster]

I would assume the following should work:
(but obviously untested)

for f in $(ls *.fastq.gz | sed 's/?_001.fastq.gz//' | sort -u)
do
java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 ${f}1_001.fastq.gz ${f}1_002.fastq.gz  ${f}_R1_paired.fq.gz ${f}1_unpaired.fq.gz ${f}_2_paired.fq.gz ${f}2_unpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
done

You can easily check if the commands look alright be adding in an echo statement:

for f in $(ls *.fastq.gz | sed 's/?_001.fastq.gz//' | sort -u)
do
echo java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 ${f}1_001.fastq.gz ${f}1_002.fastq.gz  ${f}_R1_paired.fq.gz ${f}1_unpaired.fq.gz ${f}_2_paired.fq.gz ${f}2_unpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
done

[shashankgupta]

I would assume the following should work:
(but obviously untested)

for f in $(ls *.fastq.gz | sed 's/?_001.fastq.gz//' | sort -u)
do
java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 ${f}1_001.fastq.gz ${f}1_002.fastq.gz  ${f}_R1_paired.fq.gz ${f}1_unpaired.fq.gz ${f}_2_paired.fq.gz ${f}2_unpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
done

You can easily check if the commands look alright be adding in an echo statement:

for f in $(ls *.fastq.gz | sed 's/?_001.fastq.gz//' | sort -u)
do
echo java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 ${f}1_001.fastq.gz ${f}1_002.fastq.gz  ${f}_R1_paired.fq.gz ${f}1_unpaired.fq.gz ${f}_2_paired.fq.gz ${f}2_unpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
done

Thank you for helping me.
But, somehow it is showing some error as shown below-

TrimmomaticPE: Started with arguments:
0*_R1_001.fastq.gz 0*_R2_001.fastq.gz 0_R1.trimmed_PE.fastq 0_R1.trimmed_SE.fastq 0_R2.trimmed_PE.fastq 0_R2.trimmed_SE.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:3:20 MINLEN:30
Exception in thread "main" java.io.FileNotFoundException: 0*_R1_001.fastq.gz (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:264)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:539)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
0
TrimmomaticPE: Started with arguments:
0*_R1_001.fastq.gz 0*_R2_001.fastq.gz 0_R1.trimmed_PE.fastq 0_R1.trimmed_SE.fastq 0_R2.trimmed_PE.fastq 0_R2.trimmed_SE.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:3:20 MINLEN:30
Exception in thread "main" java.io.FileNotFoundException: 0*_R1_001.fastq.gz (No such file or directory)
at java.io.FileInputStream.open0(Native Method)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.<init>(FileInputStream.java:138)
at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:264)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:539)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
0



As I understand, above script unable to find the file. So to simplify it, I rename all the file names, and now it looks like-


C1_R1.fastq
C1_R2.fastq

C2_R1.fastq
C2_R2.fastq

C3_R1.fastq
C3_R2.fastq

T1_R1.fastq
T1_R2.fastq

T2_R1.fastq
T2_R2.fastq

T3_R1.fastq
T3_R2.fastq

Therefore, the working trimmomatic command looks like,

java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 C1_R1.fastq C1_R2.fastq C1_R1_paired.fastq C1_R1_unpaired.fastq C1_R2_paired.fastq C1_R2_unpaired.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35

[carmarbla]

Thanks, this helped me!

[Louloute]

Hello all,

This code work on multiple single-end read files??

Any help please??

Many thanks

[carmarbla]

#!/bin/bash

for f1 in /path_to_your_raw_data/*.fastq.gz

do
java -jar /path_to_trimmomatic_folder/trimmomatic-0.36.jar SE -phred33 $f1 ${f1%%.fastq.gz}"trimmed_minleng50.fq.gz" ILLUMINACLIP:/path_to_trimmomatic_folder/adapters/TruSeq2-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50

done


This is what I used for the different SE files I have, basically it changes .fastq.gz for "trimmed_minleng50.fq.gz" once it is trimmed. You can edit the order and the value of the parameters. (Minimun_length, minimun quality at the end or start of the reads, different adapter files...).

[Louloute]

Many thanks Carmarbla for your reply!
Best

[wnegara]

Hi All,
just found these threads. Does the code

or f in $(ls *.fastq.gz | sed 's/?_001.fastq.gz//' | sort -u)
do
java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 ${f}1_001.fastq.gz ${f}1_002.fastq.gz ${f}_R1_paired.fq.gz ${f}1_unpaired.fq.gz ${f}_2_paired.fq.gz ${f}2_unpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
done

is need modification prior to use or it will work for any PE files?
cheers