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  • data for Maq

    Hi everyone,

    I'm looking for some real , not very big data to run maq. (preferably paired-end reads)

    I found some human sample reads, but they are huge, and I want to run maq on a relatively small set of data (I don't want to generate reads based on the reference sequence)

    I'm new to the field, and I don't even know where to look.

    --
    another question,

    I found a set of human reads here : http://yh.genomics.org.cn/
    and I've downloaded the reads, but I couldn't find the standard distance between paired-end reads.

    Is there a standard distance (for example from the device), or am I missing something? shouldn't I know the distance to for example run maq?


    Thanks a lot

  • #2
    Just take the top N lines of the human files you found. That will give you any size test file you like.

    Comment


    • #3
      thanks, but I want to be able to get a consensus sequence, and if I choose a small subset of human reads, there won't be enough coverage.

      Thanks

      Comment


      • #4
        There is always the SRA


        Insert size is based on the library prep, but always is variable.

        Comment


        • #5
          Thanks,

          I have a couple of dump questions, I think I'm lost in SRA.

          for example, in one entry, in description part it says :

          .... We generated two sequencing libraries. The first had a median insert size of 200 bp and was produced following .... This library was used for generating most of the data (38x coverage).
          a 200 bp insert size means the distance between paired reads is 200 or read1+distance+read2 = 200? or something else?
          The second library provided longer range paired-read information... Paired-end sequencing of the two libraries was carried out using the Illumina Genome Analyzer. ... The data contain 3.77 billion PF reads from the short-insert library and 296 million PF reads from the long-insert library.
          and there are a couple of files,
          how I am supposed to know which one is which? what is the difference between for example first and second set of files? (they both seem to be from smaller library)

          the link is : http://www.ncbi.nlm.nih.gov/Traces/s...tudy=SRP000239

          I really appreciate your help,
          I've spent some time but I couldn't make sense of it

          Comment

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