Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Maq Segmentation fault

    I'm trying to use Maq software but i've face with some problems.

    1. Conversion of *qseq.txt files (obtained after demultiplexing) to fastq (illumina) format. For doing this operation i've used this script:

    #!/usr/bin/perl

    use warnings;
    use strict;

    while (<>) {
    chomp;
    my @parts = split /\t/;
    print "@","$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
    print "$parts[8]\n";
    print "+","$parts[0]:$parts[2]:$parts[3]:$parts[4]:$parts[5]#$parts[6]/$parts[7]\n";
    print "$parts[9]\n";
    }
    2. Conversion of the "fastq illumina" files just get at point 1 to "fastq sanger format".

    For doing this i've tryied to different approaches:
    • Patching Maq with maq_ill2sanger.patch
    • Using the script called fq_all2std.pl with the command "sol2std"
    • Using the script in attachment called qseq2fastqsang.pl


    3. After converting reads (fastq sanger) and reference sequence (fasta format) to .bfg and .bfa respectively, i've tried to perform the mapping with the "match command" but i got segmentation fault.

    How can solve this problem?

    I've tried both 0.7.1 and 0.6.8 version but nothing change.

    Which is the faulty step? Where i'm getting wrong?

    Thanks in advance!
    Attached Files

  • #2
    I've solved the problem

    Greetz

    Comment


    • #3
      Originally posted by Seq84 View Post
      I've solved the problem

      Greetz
      How? I'm having the same issue

      Comment


      • #4
        solve method

        Originally posted by Seq84 View Post
        I'm trying to use Maq software but i've face with some problems.

        1. Conversion of *qseq.txt files (obtained after demultiplexing) to fastq (illumina) format. For doing this operation i've used this script:



        2. Conversion of the "fastq illumina" files just get at point 1 to "fastq sanger format".

        For doing this i've tryied to different approaches:
        • Patching Maq with maq_ill2sanger.patch
        • Using the script called fq_all2std.pl with the command "sol2std"
        • Using the script in attachment called qseq2fastqsang.pl


        3. After converting reads (fastq sanger) and reference sequence (fasta format) to .bfg and .bfa respectively, i've tried to perform the mapping with the "match command" but i got segmentation fault.

        How can solve this problem?

        I've tried both 0.7.1 and 0.6.8 version but nothing change.

        Which is the faulty step? Where i'm getting wrong?

        Thanks in advance!
        you can split the raw reads to two or three parts and then convert the format to bfq,following,do mapping.After finishing these work,you can merge the mapping result to one file.Hope you to solve the problem soon .

        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
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        7 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
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X