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novoalign output same location twice

Posted by mav12zuki on Fri 25 of May, 2012 09:15 MYT

Hi,

I am new to this forum. I am mapping the following SE read with these options:

-f $1 -o NATIVE -R 10 -r 0.33


@HWI-ST373:3:1101:1976:1977#0/1
TAAAGGCCTAACAAAAACATTCTTGATCTGTAAATAATCTAAGCAAACCACACTAAACA

+HWI-ST373:3:1101:1976:1977#0/1

JegddZbYafaagghhdfdgaeg[XbcSY^egb`eccccb_cghagcff\_bfg\

and I am getting two alignments for it, but they are exactly the same in the NAT format. Why is this not considered a single alignment? Thanks!

@HWI-ST373:3:1101:1976:1977#0ACG_ACG/1 S TAAAGGCCTAACAAAAACATTCTTGATCTGTAAATAATCTAAGCAAACCACACTAAACA +chr1 57684652 F . . .
@HWI-ST373:3:1101:1976:1977#0ACG_ACG/1 S TAAAGGCCTAACAAAAACATTCTTGATCTGTAAATAATCTAAGCAAACCACACTAAACA +chr1 57684652 F . . .

Reads: 2933

Posted by colin on Fri 25 of May, 2012 09:43 MYT

Hi,

I just tried on hg36 an dthe problem didn't occur. Can you check you are using the latest version.

Colin

novoalign -d /wd5/db/hg36 -f r.fq -R 10 -r 0.33

  1. novoalign (V2.08.02 - Build May 18 2012 @ 09:25:21 - A short read aligner with qualities.
  2. (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
  3. License file: /home/sparks/bin/novoalign.lic
  4. Licensed to Novocraft Technologies Sdn Bhd
  5. novoalign -d /wd5/db/hg36 -f r.fq -R 10 -r 0.33
  6. Starting at Fri May 25 09:28:28 2012
  7. Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7.
  8. Index Build Version: 2.7
  9. Hash length: 14
  10. Step size: 3

@HWI-ST373:3:1101:1976:1977#0/1 S TAAAGGCCTAACAAAAACATTCTTGATCTGTAAATAATCTAAGCAAACCACACTAAACA +chr1 57457240 F . . .

  1. Read Sequences: 1
  2. Aligned: 1
  3. Unique Alignment: 1
  4. Gapped Alignment: 0
  5. Quality Filter: 0
  6. Homopolymer Filter: 0
  7. Elapsed Time: 0.003 (sec.)
  8. CPU Time: 0.0 (min.)
  9. Done at Fri May 25 09:30:32 2012
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Posted by mav12zuki on Fri 01 of June, 2012 15:43 MYT

Hi,

Thanks for responding. I was working with hg19. It seems to work when i use novoindex on genome.fa as opposed to chr*fa.

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Posted by colin on Fri 01 of June, 2012 15:58 MYT

Hi,

Perhaps you had input chr1 into Novoindex twice. It doesn't check for this and will happily index many sequences with the same name.

Glad it's sorted.
Colin

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