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SOAPdenovo map question

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  • SOAPdenovo map question

    Dear fellow sequencers,

    I am trying to assemble some reads using SOAPdenovo and map the reads to the assembled contigs. In SOAPdenovo, there is a utility SOAPdenovo map, that is supposed to do this. But when I do this, the resulting *readOnContig is empty (leave header line). The output I get from SOAPdenovo-63mer map is:

    Version 1.05: released on July 29th, 2010

    K = 31
    contig len cutoff: 33

    there're 1125597 contigs in file: test_fasta_020611, max seq len 5161, min seq len 32, max name len 10
    time spent on parse contigs file 11s
    8 thread created
    time spent on hash reads: 5s
    16173369 nodes allocated, 17130136 kmer in reads, 17130136 kmer processed
    time spent on De bruijn graph construction: 16s

    time spent on mapping long reads: 1s

    In file: config.txt, max seq len 85, max name len 256

    8 thread created
    2250827 edges in graph
    0 out of 0 (nan)% reads mapped to contigs
    no paired reads found
    [LIB] 0, avg_ins 0, reverse 0
    time spent on mapping reads: 1s

    overall time for alignment: 0m

    I am using the same config file and read file for both the assembly and the mapping. So what could be the reason for the failed mapping?


  • #2
    I have faced the same problem with you.
    Let's pray for a master-hand to give a solution.


    • #3
      Hi xysheep,

      I asked this from SOAPdenovo support back some time ago, and they told me that the map function only works with paired end reads. Hope this helps you!