Splitting the data up is exactly what I did to simplify things. You can give srma a set of ranges using the "RANGES=ranges.txt" with
e.g.
And adding "-Xmx4G" increases the memory for java to use to 4Gb. Im still not sure how much is enough based on coverage so I keep it reasonably high.
So just make a "ranges.txt" for each chromosome and launch your separate threads
e.g.
chr1 1 3224608765
chr2 1 6342342344
chr3 1 6453554555
chr2 1 6342342344
chr3 1 6453554555
So just make a "ranges.txt" for each chromosome and launch your separate threads
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