Artemis visualization of RNA-seq alignments

[ThePresident]

Hello everyone,

Juts a couple of quick questions:

1) how to increase memory usage for artemis? I tried to add java -mx250m -jar in front of my path in target field, but it just won't work. That should work (I took it from Sanger webpage), but there must be a small detail that I'm not doing right.

2) when I load sorted BAM file of RNA-seq reads against my reference genome, for some regions/genes I see some kind of peak i.e. reads seamed to reach a maximum and they are all equal (look at the picture, in red). That's certainly not normal... you guys have any idea what is it about?

3) There are two colors in my alignment in artemis (see picture). Why's that? I have single-end RNA-seq data and my libraries were not strand specific...

4) If I load two or more replicates as separate files, what artemis displays is a mean of my different biological replicates?

Thanks!

[protist]

For increasing memory edit the info.plist file in the Artemis folder. The protocol I use is for a mac but is as follows:

Artemis Memory Increase:
Open Terminal and go to Artemis in Applications folder

Emacs Info.plist
Change value as detailed below
Control XC to exit & Press Y to save

Set the value in the file Info.plist in the
directory Artemis.app/Contents. Towards the bottom of the file there are a
couple of lines that look like this:
<key>VMOptions</key>
<string>-Xmx800m</string>

Changing the value after -Xmx will change the memory used by Artemis.

[ThePresident]

Thanks for your answer. However, I'm using Artemis under windows 7, so I even can't find the info.plist

TP

[protist]

Thanks for your answer. However, I'm using Artemis under windows 7, so I even can't find the info.plist

TP

Here is info for PC - is pre 7 but try and see if you can use it...
To increase the memory allocation, create a shortcut for the Artemis program and right click on the shortcut icon. In the box which specifies the Target you will see the location of the program with which the shortcut is associated.

Place quotation marks around the target and infront of the target type: C:\WINDOWS\SYSTEM32\java.exe -jar -Xincgc -Xmx150000000 . If you are using Windows 2000 rather than Windows XP, type: C:\WINNT\SYSTEM32\java.exe -jar -Xincgc -Xmx150000000 .

[krispy]

Hi, I couldn't find a way to increase the memory. I have the artemis.jar on my desktop, and I created a shortcut to it. I tried putting in java -mx250m -jar in front of the target field but it just gave me "the name java specified in the target box is not valid". The C:\WINDOWS and C:\WINNT didn't help as well. I am using Windows 7. Can anyone help me with this, I am so confused.