Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • SOAP:segmentation fault

    Hi All,
    I am trying to map solexa PE reads (fastq) from different strains onto reference scaffolds file (fasta) using soap2. The questions I have are:
    1. The alignment works but it seems that soap is not able to read seq data from all the 8 strains I have in the command as the number of reads that it processes is too low to encompass all the 8 strains.
    2. When I try to msort (-k 8,n9) the PE output file from the alignment, it comes back with error (segmentation fault) however, the SE output gets sorted with the same command.
    3. The snp calling through soapsnp (-d <ref> -i <SEoutput.sort> -r 0.00005 –e 0.0001 -t -u -L <100>) generates a huge file many times larger than original file. Is that usual?
    Thanks for the patient reading.

  • #2
    Hi Mansequencer,

    For some reason, MSORT doesn't work with files over a certain size. It works just fine for small files using the command:
    Code:
    $ msort -k 8,n9 mapped.out > mapped.out.sort
    To get around this, you can use the SORT command that is native to most Linux and Unix distributions:
    Code:
    sort -t $'\t' -k 8f,8 -k 9n,9 mapped.out > mapped.out.sort
    To check to see if your files are indeed sorted, you can always isolate just the two columns in question, the chromosome and position:
    Code:
    cut -f 8,9 mapped.out.sort > col_89.txt
    SOAPSNP generates a huge file on purpose. Either of the other formats GLFv2 and GPFv2 may give a smaller footprint output. Try those.

    Best of luck,
    -Awesome

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X