tophat results: chr4-9 missing ??
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.
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.