Where and How to find TruSeq Universal Adapter file: TruSeq3-PE.fa

Question

[otieno43]

Hello guys,

I have some RNA-seq reads that I am trying to trim out the adapters and low quality reads using TRIMMOMATIC. I am however unable to proceed as I get into problems with lack of TruSeq3-PE.fa. I am working on the cluster. I thought that just by loading Trimmomatic, it would load with all the requirements but it looks like I don't know what is happening.

trimmomatic PE -threads 4 -phred33 TN-SN_1_107_086_S16_L002_R1_001.fastq.gz TN-SN_1_107_086_S16_L002_R2_001.fastq.gz /trimmedReads/MgSN1_R1_trimmed.fastq.gz /trimmedReads/MgSN1_R1_un-trimmed.fastq.gz /trimmedReads/MgSN1_R2_trimmed.fastq.gz /trimmedReads/MgSN1_R2_un-trimmed.fastq.gz ILLUMINACLIP:$TRIM/adapters/TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

This is what I get:

java.io.FileNotFoundException: /adapters/TruSeq3-PE.fa (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.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:536)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

Any help will be appreciated.

Answer 1

[Istvan Albert]

You can find those files on the Trimmomatic Github page:

• https://github.com/usadellab/Trimmomatic/tree/main/adapters

[otieno43]

Thanks Albert