Remove adpater from reads

Question

[priya.bmg]

Hello

I need advice on adapter trimming. I removed the Ilumina small RNA 3' adapter from my forward sequence and Ilumina Universal adapter from the reverse strand (using cutadapt). Used the adpater information from https://eurofinsgenomics.eu/media/1610545/illumina-adapter-sequences.pdf. But still could see the adapter not being removed as shown below in the fastQC report. Am I using the wrong adapter information or missing any step?

cutadapt -a ATCTCGTATGCCGTCTTCTGCTTG -o output.fastq 24_1.fastq ## remove adapter from forward strand

cutadapt -a AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -o output2.fastq 24_2.fastq ## remove adapter from reverse strand

Thanks

Priya

[GenoMax]

It appears that you have very short inserts and cutadapt is not making the initial matches. I am not a cutadapt user but you will need to decrease the initial seed match.

With bbduk.sh from BBMap suite you can try:

bbduk.sh -Xmx4g in=file.fastq out=trimmed.fastq literal=ATCTCGTATGCCGTCTTCTGCTTG,AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT  k=8 ktrim=r

[gb]

I think you need to reverse complement the adapter in this case. (Just noticed the input is two different files, forward and reverse)

EDIT:

And here more info about the parameters https://cutadapt.readthedocs.io/en/stable/guide.html#adapter-trimming-parameters You may need to change the -e and -O parameter.