Trimmomatic/ linux system

Trimmomatic/ linux system

1

Hi all,

I am trying to remove adapters and clean my RNA-seq.gz files using Trimmomatic, loaded on a Linux system (supercomputer server)

Following the steps for Pair ends reads, explained in the manual (www.usadellab.org/cms/?page=trimmomatic)

java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36

Since Trimmomatic figured out the argument, I assume Trimoomatic is loaded successfully, before starting the process!

TrimmomaticPE: Started with arguments:
 T1R1-f.fastq.gz T1R1-r.fastq.gz T1R1-f_paired.fq.gz T1R1-f_unpaired.fq.gz T1R1-r_paired.fq.gz T1R1-r_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
java.io.FileNotFoundException: /*****/project/****/md/RNA/rna_data-bacteria/TruSeq3-PE.fa (No such file or directory)
    at java.base/java.io.FileInputStream.open0(Native Method)
    at java.base/java.io.FileInputStream.open(FileInputStream.java:213)
    at java.base/java.io.FileInputStream.<init>(FileInputStream.java:155)
    at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71)
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
    at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
Quality encoding detected as phred33

Thank you in advance


Illumina


sequencing


RNA-Seq


Trimmomatic

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