BioInformatics9 Mapping - Bowtie2 & Samtools (conda) ◆ Install(python3.8환경) 1) 가상환경 설정 >>> conda create -n [환경명] python=3.8 >>> conda env list # 가상환경 리스트 출력 >>> conda activate [환경명] 2) 설치 >>> conda install bioconda::bowtie2 >>> conda install bioconda::samtools ◆ Usage 1. 가상환경 설정 >>> conda activate [환경명] 2. Reference Index >>> bowtie2-build reference.fasta 3. Mapping >>> bowtie2 -x reference.fasta -1 input_fwd.fastq -2 input_rev.fastq -S ou.. 2024. 4. 3. Mapping - BWA2 & Samtools (conda) ◆ Install >>> conda install bioconda::bwa-mem2 >>> conda install bioconda::samtools ◆ Usage 1. Reference Index >>> bwa-mem2 index -p 32GB reference.fasta 2. Mapping(Illumina) >>> bwa mem -t 1 -R "@RG\tID:[ID 이름]\tSM:[샘플이름]\tPL:ILLUMINA" reference.fasta input_fwd.fastq input_rev.fastq > output_mapped.sam * 추가설명 '@RG\tID:text\tSM:text\tPL:text' @RG - sam header 중 RG 를 쓰겠다는 뜻.. \t - tab sep.. 2024. 4. 3. Mapping - BBmap & Samtools (conda) ◆ Install >>> conda install bioconda::bbmap >>> conda install bioconda::samtools ◆ Usage 1. Reference Index >>> bbmap.sh -Xmx32g ref=reference.fasta 2. Mapping(Illumina) >>> bbmap.sh -Xmx32g in1=input_fwd.fastq in2=input_rev.fastq out=output_mapped.sam ref=reference.fasta 3. Sam -> Bam 변환 >>> samtools view -Sb output_mapped.sam > output_mapped.bam 4. Sort >>> samtools sort -o output_sort.. 2024. 4. 3. Quality Check - FastQC (conda) ◆ Install >>> conda install bioconda::fastqc ◆ Usage >>> fastqc File -> Load file(fastq) 2024. 4. 3. 이전 1 2 3 다음
