Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • construct whole genome reference for HG19

    I download HG19 from ucsc, after unzip it is many files seperated by chr.

    I did
    cat chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr20.fa chr21.fa chr22.fa chrX.fa chrY.f
    a chrM.fa >hg19.fa

    to create the hg19.fa

    then I used bwa to build the index,
    ./bwa index hg19.fa
    This step has no error either.

    Then I run bwa like this

    ./bwa aln -q 15 hg19.fa sample.txt>sample.sai

    I get this error

    [bwa_aln] 17bp reads: max_diff = 2
    [bwa_aln] 38bp reads: max_diff = 3
    [bwa_aln] 64bp reads: max_diff = 4
    [bwa_aln] 93bp reads: max_diff = 5
    [bwa_aln] 124bp reads: max_diff = 6
    [bwa_aln] 157bp reads: max_diff = 7
    [bwa_aln] 190bp reads: max_diff = 8
    [bwa_aln] 225bp reads: max_diff = 9
    [bwa_read_seq] 0.0% bases are trimmed.
    [bwa_aln_core] calculate SA coordinate... Segmentation fault


    Does anyone know what could have caused this error?

  • #2
    Originally posted by foxyg View Post
    I download HG19 from ucsc, after unzip it is many files seperated by chr.
    […]

    Does anyone know what could have caused this error?
    If you run
    Code:
    $ bwa index
    you'll see this note:

    Code:
    Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
             `-a div' do not work not for long genomes. Please choose `-a'
             according to the length of the genome.
    hence you can fix it indexing like this:

    Code:
    $ bwa index -a bwtsw hg19.fa
    d

    Comment


    • #3
      Thanks I am trying this. But I have built index for single chr before without using -a option and it worked out fine.

      Comment


      • #4
        Originally posted by foxyg View Post
        Thanks I am trying this. But I have built index for single chr before without using -a option and it worked out fine.
        A single chrom is probably small enough for default "is" algorithm

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 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