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  • Average insert size from paired end data

    Hi there!

    I am searching for a way to get the average insert size from my data, that was not included.
    The dataset i am using is paired-end Illumina data and I ran BLAST.

    Has someone a clue or an idea how to get the average insert size from my data?
    Is there maybe a simple solution or even a command for this?

    Best regards,
    Petrichor.

  • #2
    If you use a standard aligner (bowtie, bwa, etc.) on a small chunk of the data, the resulting SAM file will contain insert sizes for all of the mapped reads. You could then just average that with awk or perl or whatever you like.

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    • #3
      BLAST? On Illumina data? Why didn't you use a short read aligner?

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      • #4
        You can only use a short-read aligner if you have a reference, as dpryan suggested. Use the paired-end option of the aligner. If you do not have a close reference, make a quick-and-dirty assembly of a subset of your data. Next, align your paired-end reads to the assembly and obtain the insert-size. Third option, probably the quickest, is to ask for the insert size at your sequence provider

        Regards,
        Boetsie

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        • #5
          Thanks for the responds!

          Changed to bowtie2 and used some short awk-commands.
          Got some results, hope they will work.

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