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IGV

build index

  1. bowtie2-build --threads 8 genome.fa genome.fa

build sam file

  1. bowtie2 -p 8 -q --no-unal -k 20 -x genome.fa -U reads.fq   -S  bowtie2.sam
  2. bowtie2 -p 8 -q --no-unal -k 20 -x genome.fa -1 reads_1.fq -2 reads_2.fq  -S  bowtie2.sam
  4. ##Exp:
  5. bowtie2 -p 8 -q --no-unal -k 20 -x Trinity.fasta -U SRR771602.fastq   -S  bowtie2.sam

sam to bam

  1. samtools view -b -S bowtie2.sam > bowtie2.bam
  2. samtools sort bowtie2.bam -o bowtie2.coordSorted.bam > bowtie2.coordSorted.bam
  3. samtools index bowtie2.coordSorted.bam
  4. samtools faidx Trinity.fasta

IGV

  1. ~/Biosoft/IGV_2.4.10/igv.sh -g Trinity.fasta bowtie2.coordSorted.bam

Enjoy~

本文由Python腳本GitHub/語雀自動更新

由於語法渲染問題而影響閱讀體驗， 請移步博客閱讀～
本文GitPage地址

GitHub: Karobben
Blog:Karobben
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