Hi,
I ran a sample through novoalign (# novoalign (2.06.09MT - Jun 16 2010 @ 12:36:05)) and the mapping stats were as follows;
# Paired Reads: 15258295
# Pairs Aligned: 13278014
# Read Sequences: 30516590
# Aligned: 30005116
# Unique Alignment: 27625593
# Gapped Alignment: 321486
# Quality Filter: 108560
# Homopolymer Filter: 64
# Elapsed Time: 5472,836s
I then ran the same sample through the MPI version of novoalign (# novoalignMPI (V2.07.11 - Build May 27 2011 @ 15:31:23 on a difference computational cluster) and got the following stats:
# Paired Reads: 15258295
# Pairs Aligned: 13138914
# Read Sequences: 30516590
# Aligned: 29643668
# Unique Alignment: 27110885
# Gapped Alignment: 258400
# Quality Filter: 222384
# Homopolymer Filter: 2105
# Elapsed Time: 881.205 (sec.)
# CPU Time: 545.9 (min.)
The number of sequences aligned is lower but in general the values are similar except for the homopolymer filter which is quite different 64 verus 2105.
Can anyone tell me...
what is an expected number for the homopolymer filter?
Should I be worried that the numbers are so different?
Does it seem right that fewer sequences aligned or should I expect exactly the same numbers?
Is this likely to be due to different versions of novoalign?
or the single verus multithreaded MPI version?
I'd be glad of any input.
Thanks,
Jane
I ran a sample through novoalign (# novoalign (2.06.09MT - Jun 16 2010 @ 12:36:05)) and the mapping stats were as follows;
# Paired Reads: 15258295
# Pairs Aligned: 13278014
# Read Sequences: 30516590
# Aligned: 30005116
# Unique Alignment: 27625593
# Gapped Alignment: 321486
# Quality Filter: 108560
# Homopolymer Filter: 64
# Elapsed Time: 5472,836s
I then ran the same sample through the MPI version of novoalign (# novoalignMPI (V2.07.11 - Build May 27 2011 @ 15:31:23 on a difference computational cluster) and got the following stats:
# Paired Reads: 15258295
# Pairs Aligned: 13138914
# Read Sequences: 30516590
# Aligned: 29643668
# Unique Alignment: 27110885
# Gapped Alignment: 258400
# Quality Filter: 222384
# Homopolymer Filter: 2105
# Elapsed Time: 881.205 (sec.)
# CPU Time: 545.9 (min.)
The number of sequences aligned is lower but in general the values are similar except for the homopolymer filter which is quite different 64 verus 2105.
Can anyone tell me...
what is an expected number for the homopolymer filter?
Should I be worried that the numbers are so different?
Does it seem right that fewer sequences aligned or should I expect exactly the same numbers?
Is this likely to be due to different versions of novoalign?
or the single verus multithreaded MPI version?
I'd be glad of any input.
Thanks,
Jane
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