IGV

IGV

Dowload

https://software.broadinstitute.org/software/igv/download

open:

bash igv.sh

build index

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

build sam file

bowtie2 -p 8 -q --no-unal -k 20 -x genome.fa -U reads.fq   -S  bowtie2.sam
bowtie2 -p 8 -q --no-unal -k 20 -x genome.fa -1 reads_1.fq -2 reads_2.fq  -S  bowtie2.sam

##Exp:
bowtie2 -p 8 -q --no-unal -k 20 -x Trinity.fasta -U SRR771602.fastq   -S  bowtie2.sam

sam to bam

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

IGV

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