Hope all of you are doing good :)
This is a two part question,
- I get the following error when trying to use hg38 to plot my bam files.
INFO [2021-06-30 11:29:58,978] [Main.java:154] Startup IGV Version 2.4.10 03/20/2018 10:50 PM INFO [2021-06-30 11:29:59,015] [Main.java:155] Java 10.0.2 INFO [2021-06-30 11:29:59,017] [DirectoryManager.java:76] Fetching user directory... INFO [2021-06-30 11:30:00,177] [Main.java:156] Default User Directory: /home/urangasw INFO [2021-06-30 11:30:00,179] [Main.java:157] OS: Linux INFO [2021-06-30 11:30:02,839] [Main.java:202] A later version of IGV is available (2.9.4) INFO [2021-06-30 11:30:31,788] [GenomeManager.java:186] Loading genome: /home/urangasw/igv/genomes/hg19.genome INFO [2021-06-30 11:30:40,862] [GenomeComboBox.java:79] Enter genome combo box INFO [2021-06-30 11:30:40,883] [GenomeManager.java:275] Genome loaded. id= hg19 INFO [2021-06-30 11:30:41,130] [CommandListener.java:120] Listening on port 60151 INFO [2021-06-30 11:30:41,340] [BatchRunner.java:72] Executing Command: new INFO [2021-06-30 11:30:53,910] [CommandExecutor.java:235] OK INFO [2021-06-30 11:30:53,911] [BatchRunner.java:72] Executing Command: genome hg38 INFO [2021-06-30 11:30:53,913] [IGVCommandBar.java:165] Selecting genome hg38 INFO [2021-06-30 11:31:03,572] [MessageUtils.java:74] ERROR: Could not locate genome: hg38 INFO [2021-06-30 11:31:05,573] [CommandExecutor.java:235] ERROR: Could not locate genome: hg38 INFO [2021-06-30 11:31:05,574] [BatchRunner.java:72] Executing Command: snapshotDirectory
/home/urangasw/Softwares/IGV-snapshot-automator-master/analysis_3 INFO [2021-06-30 11:31:07,576] [CommandExecutor.java:235] OK
The final snapshots are done using hg19 since hg38 was not located. My question here is, is the IGV version of hg38 genome available for download? If so, where? If not, what's the alternative?
- How to change the track color of the coverage in IGV while using batch script? Suppose I have 4 cases and 4 controls, I want the coverage of cases to be red and controls to be blue. I know there is the colorby option as one of the batch command, but little is given about how to use it effectively.
I'll be glad if somebody can help me out with these problems. Have a lovely day.