I've just used trim_galore (arguments below) to trim the adapter sequences off of fastq files from Illumina hiseq 4000 run TruSeq prep. Cutadapt seemed to work well, running it in the default mode to auto-detect adapters and remove them, as well as remove any bases with phred score < 5, but my fastQC reports for some files show that Illumina Single End PCR primer or TruSeq Adapter, Index 7, remain in certain samples (0.15 % and 0.53 %, respectively).
Do I have to run cutadapt again and feed it these specific sequences to remove? I have many samples and searching through each report for specific adapters to remove in a second cutadapt run is not ideal.
Was I not stringent enough in trimming?
Do I need to get rid of the remaining contaminants to perform differential gene expression analysis?
trim_galore --paired -q 5 -o /output/path/ --fastqc_args "--outdir /fastqc/output/path/" sample_R1.fastq.gz sample_R2.fastq.gz
Do I have to run cutadapt again and feed it these specific sequences to remove? I have many samples and searching through each report for specific adapters to remove in a second cutadapt run is not ideal.
Was I not stringent enough in trimming?
Do I need to get rid of the remaining contaminants to perform differential gene expression analysis?
trim_galore --paired -q 5 -o /output/path/ --fastqc_args "--outdir /fastqc/output/path/" sample_R1.fastq.gz sample_R2.fastq.gz
Comment