trim_galore2 [Trim Galore] RNA-Seq data trimming (default option) paired-end default option trim_galore --paired fastq_1.fastq fastq_2.fastq --gzip -o /output_directory --paired: paired-end인 경우, 그리고 순서대로 fastq file을 넣어준다 --gzip: fastq파일로 저장하면 크기때문에 압축 (optional) -o: output 저장경로 지정 Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.8 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASC.. 2022. 10. 2. bowtie2, trim_galore 반복문 (trimming & mapping for multiple sequence) trim_galore for i in *.fastq do base=$(basename $i _1.fastq) trim_galore --paired ${base}_1.fastq ${base}_2.fastq -o /output_directory done bowtie2 (mapping 후 bam file 변환까지) for i in *1.fastq do base=$(basename $i _1.fastq) bowtie2 -p 8 -x reference -1 ${base}_1.fastq -2 ${base}_2.fastq | samtools view -b -o ${base}.bam - done https://stackoverflow.com/questions/64638763/applying-restriction-of-.. 2022. 9. 27. 이전 1 다음