Question: memory is low reading termination?
0
gravatar for barrypraveen
18 months ago by
barrypraveen20
barrypraveen20 wrote:

I have lots of BAM file. I am looking novel transcripts from my bam file by using IGV. I have 4gb (Linux) and 8 GB Windows 10 systems. I want to allocate more RAM memory for IGV help me how to proceed.

rna-seq next-gen alignment • 1.4k views
ADD COMMENTlink modified 18 months ago by genomax75k • written 18 months ago by barrypraveen20
2
gravatar for genomax
18 months ago by
genomax75k
United States
genomax75k wrote:

On Windows there is an igv.bat batch file that you must be using to start IGV. You could edit this line

jre1.8.0_NNN\bin\javaw  -Xmx2G -Dproduction=true -Djava.net.preferIPv4Stack=true -Dsun.java2d.noddraw=true -jar %BatchPath%lib\igv.jar  %*

and increase the -Xmx parameter to a higher value -Xmx6G. Since you only have 8G of RAM for windows you don't want to go any higher. If this does not suffice then you need to find hardware with better specs.

ADD COMMENTlink modified 18 months ago • written 18 months ago by genomax75k

Ok thanks, previously i allocated more RAM for IGV but it did not any better results.

ADD REPLYlink written 18 months ago by barrypraveen20

how many BAM files we can load. Because i have many.

ADD REPLYlink written 18 months ago by barrypraveen20

You can load many if there is ample RAM available. If you are running out of resources on your computer then you are going to be limited by as many as that can fit in the memory you can afford to spare.

ADD REPLYlink written 18 months ago by genomax75k
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