Create your own .genome file

1. Click Genomes>Create .genome File in menu bar of IGV. IGV will popup a window for entering needed information.

2. Enter an ID and a descriptive name for the genome.

3. 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 fai suffix in the same directory as the FASTA file; Or one can index genome FASTA file using samtools faidx genome.fasta.

4. Optionally, specify the cytoband file and the annotation (gene) file.
   • cytoband can be downloaded from UCSC like http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/
   • Annotation file should be GTF format. It can be the file generated by cufflinks or cuffcomapre. General GTF file can be downloaded using UCSC Table Browser.

5. If the sequence (chromosome) names differ between your FASTA and annotation files, you might need to create an alias file 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 chr to the name, for example  1 > chr1 and 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_002229.3 in the corresponding GFF file.

6. Click Save and select the directory in which to save the genome archive (*.genome).

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

IGV批量截图时包含红色标记区域

• 自动截图前，先把要截图的区域导入，然后再运行batch script