Hello.
I submitted this into trimmomatic to do QC.
Yet, I know that there are lots of adapters in my sequence based on the duplication results which is normal for RNAseq.
However, I am not sure if this command will cut out the adapters, or if I should use the "ILLUMINACLIP" command to explicitly cut the adapter.
Here is my trimmomatic command
java -classpath /auto/rcf-proj/sa1/software/Trimmomatic-0.22/trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 16 -phred33 CHLA-122_S3_R1.fastq.gz CHLA-122_S3_R2.fastq.gz paired_trimmed_CHLA-122_S3_R1.fastq.gz unpaired_trimmed_CHLA-122_S3_R1.fastq.gz paired_trimmed_CHLA-122_S3_R2.fastq.gz unpaired_trimmed_CHLA-122_S3_R2.fastq.gz SLIDINGWINDOW:4:20 MINLEN:30
I submitted this into trimmomatic to do QC.
Yet, I know that there are lots of adapters in my sequence based on the duplication results which is normal for RNAseq.
However, I am not sure if this command will cut out the adapters, or if I should use the "ILLUMINACLIP" command to explicitly cut the adapter.
Here is my trimmomatic command
java -classpath /auto/rcf-proj/sa1/software/Trimmomatic-0.22/trimmomatic-0.22.jar org.usadellab.trimmomatic.TrimmomaticPE -threads 16 -phred33 CHLA-122_S3_R1.fastq.gz CHLA-122_S3_R2.fastq.gz paired_trimmed_CHLA-122_S3_R1.fastq.gz unpaired_trimmed_CHLA-122_S3_R1.fastq.gz paired_trimmed_CHLA-122_S3_R2.fastq.gz unpaired_trimmed_CHLA-122_S3_R2.fastq.gz SLIDINGWINDOW:4:20 MINLEN:30
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