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Update Week4_Trimming.md
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theheking authored Mar 1, 2024
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Expand Up @@ -78,9 +78,9 @@ We will use only a few of these options and trimming steps in our analysis. It i

However, a complete command for Trimmomatic will look something like the command below. This command is an example and will not work, as we do not have the files it refers to:

$ trimmomatic PE -threads 4 SRR_1056_1.fastq SRR_1056_2.fastq \
SRR_1056_1.trimmed.fastq SRR_1056_1un.trimmed.fastq \
SRR_1056_2.trimmed.fastq SRR_1056_2un.trimmed.fastq \
$ trimmomatic PE -threads 4 EXAMPLE_1.fastq EXAMPLE_2.fastq \
EXAMPLE_1.trimmed.fastq EXAMPLE_1un.trimmed.fastq \
EXAMPLE_2.trimmed.fastq EXAMPLE_2un.trimmed.fastq \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
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