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  • 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

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