#19 Different qualities on different platforms

closed
nobody
None
5
2009-08-20
2009-06-21
Anonymous
No

hello,

I am a newbie in maq, I use maq version 0.7.1 to align short reads(36 bp) to a reference genome. I used the same binary and the same command line on two platforms and got different scores (55 vs 0).

I am using two platforms, both on linux environment:
1. Intel(R) Xeon(R) CPU X5472 @ 3.00GHz (my local pc)
2. Quad-Core AMD Opteron(tm) Processor 2354 (a head on a cluster)

The commands I ran :
maq match local_math13_all_from_seq_seed_100.map../all.bfa seq.bfq -s 100
maq match cluster_n003_all_from_seq_seed_100.map ../all.bfa seq.bfq -s 100

The results were:
maq mapview local_math13_all_from_seq_seed_100.map
SEQ chr12 97780836 + 0 0 55 55 55 0 0 1 0 36 GACAAAACCAGGAATGGGAATAACATTTGAAATGTAVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV
maq mapview cluster_n003_all_from_seq_seed_100.map
SEQ chr12 97780836 + 0 0 0 0 0 0 0 1 0 36 GACAAAACCAGGAATGGGAATAACATTTGAAATGTAVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV

I dont want to send the all.bfa file because its 1.3 GB. I didn't succeed in finding an example with a smaller reference.
If you want to get it, its the reference genome of a mouse in the mm9 version(of all the chromosomes together).

Thanks in advance,
Yoav Voichek

Discussion

  • Nobody/Anonymous

     
    Attachments
  • lh3

    lh3 - 2009-08-20

    In mapping, maq has a random behaviour which may affect a tiny fraction of reads in a uniform way. It occrs very rarely. I would suggest ignoring this in general.

     
  • lh3

    lh3 - 2009-08-20
    • status: open --> closed
     

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