Trimmomatic RNAseq Adapter Cut

[arcolombo698]

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

[arcolombo698]

Adapter Cut

The other question I have is, I have a higher variance in quality for the first 10 base pairs.

If I cut the first ten base pairs, is that equivalent to cutting out the adapters?

I am under the impression that the adapters are on the "ends" of the sequence.

[tokikake]

Hi,
I would recommend to use the ILLUMINACLIP command; if your fragments are short you will sequence through you fragment and into the 3' adapter. It depends on your library prep and of course of the length of your reads.
Of course you can use cutadapt to get a hint how many adapters are in your dataset.

Sonja