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  • mastal
    replied
    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.

    Leave a comment:


  • pic79
    replied
    assembly velvet

    Hi vishnuamaram,

    thank you for your reply.

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



    Thanks

    Leave a comment:


  • vishnuamaram
    replied
    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.

    Leave a comment:


  • pic79
    started a topic Assembly_velvet

    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

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