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Old 08-30-2010, 03:35 AM   #1
Location: Maryland

Join Date: Jul 2010
Posts: 25
Question tophat results: chr4-9 missing in "junctions.bed" file??

I have a dataset of 130 million pairs of 75bp reads.
The results are normal when I divided the set into 10 small parts and do the mapping (to hg19) separately.
But I always had chr4-9 missing in the "junctions.bed" file (the other 2 output files have all the chromosomes) if I map the whole set altogether. I reserve a memory of 4G*8 (8 threads) for this run, and the machine reports "Max vmem = 3.541G" after the job is finished, which means the 4G is enough.
Any idea why this is happening?
Thank you in advance.

Last edited by IrisZhu; 08-30-2010 at 03:42 AM.
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