Overrepresented sequence and trimming

Question

[hyejo]

Hello, I ran CRISPR/CAS9 whole genome screening. The NGS was done by HiSeqX and TruSeqDNA library.

Two of my samples resulted in low mapping ratio, so I did FastQC. I found that there were overrepresented sequences, so I think I should remove them.

Sequence Count Percentage TCGATAGCAATTCGCTTTATATATCTTGTGGAAAGGACGAAACACCCACT 68852399 42.49 No Hit

I did cutadapt using the exact same sequence. cutadapt -a TCGATAGCAATTCGCTTTATATATCTTGTGGAAAGGACGAAACACCCACT -o output.fastq.gz 2nd_2_Control_1.fastq.gz

However, I don't get the result what I expected even after trimming, still resulting low mapping rate. I am looking for a solution for my trimming process.

Thanks in advance!!!

[GenoMax]

You may want to use a proper tool designed to handle CRISPRseq data: https://github.com/afombravo/2FAST2Q