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  • issues with SOAPdenovo

    Hello.
    I am wondering if anyone here some some experience with SOAPdenovo.

    I am trying to assembly Illumina data, I have 3 lanes of 101 cycle PE data and 2 lanes of single read data.

    I have tried all sorts of options for running the program down to the default ./SOAPdenovo63mer all -s SOAPdenovo_config.txt -o out_

    At the end of the day (ok, only 2 hours), it is telling me 'no paired reads found' and tossed a terminal error.

    I have used this same data in both CLC and Velvet and it works fine including scaffolding in Velvet and paired mapping in CLC.

    I am sure I am doing something silly. Any thoughts?

    Thanks,
    Bob

    ps. my config file is:

    #maximal read length
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=1
    #in which order the reads are used while scaffolding
    rank=1
    p=/common/groups/Illx/Genomic_SIPES_lane5_1_paired_trimmed_paired.fastq
    p=/common/groups/Illx/Genomic_SIPES_lane6_1_paired_trimmed_paired.fastq
    p=/common/groups/Illx/Genomic_SIPES_lane7_1_paired_trimmed_paired.fastq
    q=/common/groups/Illx/Unpaired_SIPES_PF_lane5_1_trimmed.fastq
    q=/common/groups/Illx/Unpaired_SIPES_PF_lane7_1_trimmed.fastq

  • #2
    It has been a while since I looked at SOAPdenovo, but could you try this config ?
    ----
    #maximal read length
    max_rd_len=100
    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=1
    #in which order the reads are used while scaffolding
    rank=1
    q=/common/groups/Illx/Unpaired_SIPES_PF_lane5_1_trimmed.fastq
    q1=/common/groups/Illx/Unpaired_SIPES_PF_lane7_1_trimmed.fastq

    [LIB]
    #average insert size
    avg_ins=200
    #if sequence needs to be reversed
    reverse_seq=0
    #in which part(s) the reads are used
    asm_flags=3
    #in which order the reads are used while scaffolding
    rank=2
    q=/common/groups/Illx/Genomic_SIPES_lane5_1_paired_trimmed_paired.fastq
    q1=/common/groups/Illx/Genomic_SIPES_lane6_1_paired_trimmed_paired.fastq
    q2=/common/groups/Illx/Genomic_SIPES_lane7_1_paired_trimmed_paired.fastq

    Comment


    • #3
      Thanks.

      Unfortunately, it appears as though it was a case of RTFM more carefully. Paired reads have to be in fast-a format if in a single file. I only wasted 2 days because I didn't see that earlier. =/

      Comment

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