I received a script from a colleague and I'm figuring out how samplelist.txt looks like.


    cat samplelist.txt |parallel -j 6 --verbose --progress java -jar $(TRIMMOMATIC) PE -threads 4 -phred33 {}_R1.fastq.gz {}_R2.fastq.gz {}_R1.fq.gz {}_U_R1.fq.gz {}_R2.fq.gz {}_U_R2.fq.gz ILLUMINACLIP:trimSeq.fasta:2:7:7 MINLEN:20

These are the fastq files the script is intended to trim:

    WT_11-3_R1.fastq.gz
    WT_11-3_R2.fastq.gz
    WT_12-8_R1.fastq.gz
    WT_12-8_R2.fastq.gz
    WT_9-30_R1.fastq.gz
    WT_9-30_R2.fastq.gz
    delta_G_11-3_R1.fastq.gz
    delta_G_11-3_R2.fastq.gz
    delta_G_12-8_R1.fastq.gz
    delta_G_12-8_R2.fastq.gz
    delta_G_9-30_R1.fastq.gz
    delta_G_9-30_R2.fastq.gz
In ideal case it should be One sample name per line.

    WT_11-3
    WT_12-8
    WT_9-30
    delta_G_11-3
    delta_G_12-8
    delta_G_9-30