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  • sowmyai
    Member
    • Jan 2010
    • 27

    #1

    Paired end or not ?

    Hi

    I am very new to sequencing and bioinformatics in general. I have been tasked with de novo sequencing of many short reads of a microbe. I thought I'd start out with Velvet. Just by looking at the input, I am not able to make out if they are paired end reads or not, or what format they are (fasta, eland etc).
    My file looks like this: Many lines of 35-long nucleotides with a number after each (anywhere between 1 and 65 I think these are the number of repeated reads).

    Could someone help me with the input format - is it paired end ? fasta ? What is this ?

    Thanks
  • Bardj
    UB Buffalo Bioinformatics
    • Nov 2009
    • 26

    #2
    It may be beneficial if you could paste a segment of the file you are looking at. I know for me it helps to see a visual, so I can compare to other files that I have.

    Comment

    • sowmyai
      Member
      • Jan 2010
      • 27

      #3
      Attttttttttttctttttttttatctatttatttt 1
      aggctggaagctgccttcaacttgagatcggaagag 1
      aaagtgtgcggagcgcccccttgtgtcatcggaggg 65
      tccagttacaacctaaccaattgcccagcggtggcc 2

      Comment

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