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  • Assembly_velvet

    Hi there,

    I am currently working with illumina data. I have three different lanes.
    the first lane yielded a paired reads file while the other two are single end reads.
    I was thinking to assemble the reads with velvet firstly and then compare with other assembler tools.

    How do I go about it? what's the step to assemble the three lines?

    Thanks

  • #2
    Hi pic79,

    Are the three lanes consist of data of same sample.

    (1) What is your data mainly. DNA,RNA, small RNA.
    (2) Which organism
    (3) Consider all options of having a reference genome available or not.

    Then you should think of assembly or analysis.

    You can concatenate data of three lines or if you have sam/bam files you may use samtools merge option.

    Comment


    • #3
      assembly velvet

      Hi vishnuamaram,

      thank you for your reply.

      My data are cDNA from a gasteropod and (3) no a reference genome



      Thanks

      Comment


      • #4
        You can combine the three lanes of data with velvet, using the parameters -shortPaired -separate for the paired end reads and -short for the single end reads.

        Code:
        velveth ...... -shortPaired -separate lane1_R1.fastq lane1_R2.fastq -short lane2.fastq lane3.fastq
        See the velvet manual.

        Comment

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