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memory is low reading termination?

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 alignment next-gen
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updated by GenoMax GenoMax • written by PK • PK

1 answer

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.

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written by GenoMax GenoMax

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

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written by PK • PK

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

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written by PK • PK

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.

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written by GenoMax GenoMax

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