Another Japan in the World

Jun Aruga's blog.

Sequencing: Run mapping by bowtie2 and view it on IGV

Previously I ran mapping by Hisat2, and did view it by IGV

This time, I try to do mapping by another tool Bowtie2. It seems that Bowtie2 has simpler functions than Hisat2.

At first, see Bowtie2's official web site [1]. The source code on Github is here [2].



The installation is easy on Mac. I might introduce it before.

$ brew install bowtie2

That's it.

Prepare index file.

To do mapping by Bowtie2, the index file for the reference genome is necessary. The file can be created by bowtie2-build command from the raw reference genome file [3]. But this time, just download the file from the Bowtie2 official web site [1]. Go to [1]. Then right side Indexes section "H. sapiens, UCSC hg19", click or copy the linked URL.

$ wget

$ unzip

$ mkdir hg19

$ mv <extracted_files> hg19/

The files are like this.

$ ls /Users/jun.aruga/doc/dev/bio/reference_genome/hg19/hg19*
$ cd /path/to/read_files_directory

$ mkdir bowtie2_out

Then run mapping. The command line options are same with Hisat2.

$ bowtie2 -x /Users/jun.aruga/doc/dev/bio/reference_genome/hg19/hg19 -1 SRR747784_1_val_1.fq -2 SRR747784_2_val_2.fq -S bowtie2_out/SRR747784.sam
847491 reads; of these:
  847491 (100.00%) were paired; of these:
    48974 (5.78%) aligned concordantly 0 times
    714077 (84.26%) aligned concordantly exactly 1 time
    84440 (9.96%) aligned concordantly >1 times
    48974 pairs aligned concordantly 0 times; of these:
      451 (0.92%) aligned discordantly 1 time
    48523 pairs aligned 0 times concordantly or discordantly; of these:
      97046 mates make up the pairs; of these:
        90541 (93.30%) aligned 0 times
        3201 (3.30%) aligned exactly 1 time
        3304 (3.40%) aligned >1 times
94.66% overall alignment rate


View the outputted sam file

Menu: Tools -> Run igvtools

Command: Sort
Input file: SRR747784.bam
Output file: SRR747784.sorted.sam
Command: Index
Input file: SRR747784.sorted.sam

=> SRR747784.sorted.bam.sai is created.

Menu: File -> Load from file Specify SRR747784.sorted.sam.