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!!!