BioInformatics/Linux_Tools8 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. Trimming - Trimmomatic & BBduk (conda) ▶ Trimmomatic ◆ Install >>> conda install bioconda::trimmomatic ◆ Usage >>> trimmomatic PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15 ◆ Parameter MINLEN : 최소 남기는 염기 수 LEADING : 5’부터 염기 1개씩 품질 체크 TRALING : 3’부터 염기 1개씩 품질 체크 SLID.. 2024. 4. 1. 이전 1 2 다음
