1. 打開IGV
終端打開IGV
module load igv
module show igv
提示以下信息
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/depot/bioinfo/apps/modules/igv/2.3.60:
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
whatis("Visualization tool for interactive exploration of genomic datasets ")
load("java")
prepend_path("PATH","/group/bioinfo/apps/apps/IGV_2.3.60")
help([[
Notes:
IGV (Integrative Genomics Viewer)
version 2.3.60
Visualization tool for interactive exploration of genomic datasets
http://www.broadinstitute.org/software/igv/home
User Guide: http://www.broadinstitute.org/software/igv/UserGuide
FAQ: http://www.broadinstitute.org/software/igv/FAQ
Forum: https://groups.google.com/forum/#!forum/igv-help
Info: /group/bioinfo/apps/apps/IGV_2.3.60/readme.txt
Start with "igv.sh"
Need X11 display: More config info at:
https://www.rcac.purdue.edu/compute/carter/guide/#accounts_login_x11
]])
提示打開IGV通過igv.sh巾陕， 輸入
igv.sh &
2. 搭配使用igvtools
module load igvtools
module show igvtools
提示以下信息
----------------------------------------------------------------------------
/depot/bioinfo/apps/modules/igvtools/2.3.60:
----------------------------------------------------------------------------
whatis("Utilities for preprocessing data files ")
load("java")
prepend_path("PATH","/group/bioinfo/apps/apps/IGVTools-2.3.60")
help([[
Notes:
IGV Tools
version 2.3.60
Utilities for preprocessing data files
http://www.broadinstitute.org/software/igv/home
User Guide: http://www.broadinstitute.org/software/igv/UserGuide
FAQ: http://www.broadinstitute.org/software/igv/FAQ
Forum: https://groups.google.com/forum/#!forum/igv-help
Info: /group/bioinfo/apps/apps/IGVTools-2.3.60/igvtools_readme.txt
Need X11 display for igvtools_gui
]])
3. 加載基因組
Genomes > Load Genome form file耻台，例如Zea_mays.AGPv3.22.dna.genome.fa，加載完基因組后會生成Zea_mays.AGPv3.22.dna.genome.fa.fai的文件。
4. 加載GFF文件
由于 GFF 文件很大路操，需要排序以及建索引之后才能導(dǎo)入 IGV: 利用 IGVtools 進(jìn)行排序和建立索引
igvtools sort zea_mays.protein_coding.gff zea_mays.protein_coding.sorted.gff
igvtools index zea_mays.protein_coding.sorted.gff
load GFF 選擇剛剛排序和索引之后的 gff 文件:
點擊:file->load from file
4. 加載bam文件
BWA出來的sam文件無法直接被 IGV 利用的源譬，必須經(jīng)過 samtools 處理后才能被 IGV 顯示出來。
使用腳本批量index文件
#!/bin/bash
for i in *.bam
do
echo "Indexing: "$i
samtools index $i $i".bai"
done
注意將.bam和.bai放在同一個文件夾下壹置。
建立完索引后 load bam 文件:
File –>load from file 打剛剛建立完索引的 bam 文件竞思。
5. IGV可視化基因
找到自己感興趣基因的起始和終止位置，可以根據(jù)gff的文件進(jìn)行查找钞护「桥纾可視化結(jié)果：
