IGV and IGVtools usage
Create your own .genome file
Create .genome Filein menu bar of IGV. IGV will popup a window for entering needed information.
Enter an ID and a descriptive name for the genome.
Enter the path on your file system or a web URL to the FASTA file for the genome. If the FASTA file has not already been indexed, an index will be created during the import process. This will generate a file with
faisuffix in the same directory as the FASTA file; Or one can index genome FASTA file using
samtools faidx genome.fasta.
- Optionally, specify the cytoband file and the annotation (gene) file.
cytobandcan be downloaded from UCSC like http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/
- Annotation file should be GTF format. It can be the file
cuffcomapre. General GTF file can be downloaded using UCSC Table Browser.
If the sequence (chromosome) names differ between your FASTA and annotation files, you might need to create an
aliasfile to provide a mapping between the different names. Certain well-known aliases are built into IGV and do not require an alias file. These include mappings that involve adding or removing the prefix
chrto the name, for example
1 > chr1and
chr1 > 1. Also, NCBI identifiers of the form
gi|125745044|ref|NC_002229.3|in a FASTA file will be mapped to names of the form
NC_002229.3in the corresponding GFF file.
Saveand select the directory in which to save the genome archive (
Transfer BAM file to tdf or wig (Index BAM first)
igvtools count --strands first --includeDuplicates rnaseq.bam rnaseq.tdf,rnaseq.wig mm9 igvtools count --strands first --includeDuplicates --pairs -w 1 rnaseq.bam rnaseq.tdf,rnaseq.wig mm9
- 自动截图前，先把要截图的区域导入，然后再运行batch script