...
The easiest way to to this is probably to copy everything you want to transfer into a new directory called IGV_export. Since many of the tutorial output files had the same names (but resided in different directories) be careful to give them unique destination names when you copy them into the new directory together. To ensure you don't overwrite things be sure to use the -n command on or -i option with the cp option.While your instinct may be to use the cd command for much of this, try to stick to using the cp -n command with For starters, you could change into your mapping directory and run commands like these if you just came from the mapping tutorial:command. The difference comes from different versions of linux having slightly different cp command options. The -n command will not allow you to overwrite files, while the -i command will prompt you before overwriting anything.
| Code Block |
|---|
mkdir IGV_export cp -ni NC_012967.1.gbk.gff IGV_export # copy the new file you just converted to the export directory cp -ni $SCRATCH/bowtie2MappingTutorial/bowtie2/NC_012967.1.fasta IGV_export cp -ni $SCRATCH/bowtie2MappingTutorial/bowtie2/NC_012967.1.fasta.fai IGV_export cp -ni $SCRATCH/bowtie2MappingTutorial/bowtie2/SRR030257.sorted.bam IGV_export/bowtie.sorted.bam cp -ni $SCRATCH/bowtie2MappingTutorial/bowtie2/SRR030257.sorted.bam.bai IGV_export/bowtie.sorted.bam.bai tar -czvf IGV_export.tar.gz IGV_export |
...
| Warning |
|---|
For the remainder of the tutorial, work on your local machine. NOT TACC! |
There are two multiple ways ; Launching IGV in your web browser or by downloading the binaries locally and running IGV from your machine.to launch IGV on a local computer, in decreasing order of recommendation due to recent mac OS updates and easy of use:
| Expand | ||
|---|---|---|
| ||
Click here to download and install the mac application version |
| Expand | |||
|---|---|---|---|
| |||
This downloads the IGV executable and tells the command line to launch it (via the java command).
|
In a Web browser
Navigate a web browser to this page:http://www.broadinstitute.org/software/igv/download. You will need to register your email address to use this option!Go , but in years of registration I have never noticed any emails from them. Go ahead and click on the "Launch with 2 GB" option. This will download a "Java Web Start" file that you can launch by locating it on your Desktop and double-clicking.
| Warning | ||
|---|---|---|
| ||
This will not work on recent Mac OS updates without modifying security permissions. Recommended to use directions above. |
Locally on a Mac or Windows computer
...