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  • frequency distribution plot

    Hi!!

    I have some .sff files from a 454 sequencing proyect. I wonder if someone can help me in giving me an idea of how to plot the frequency distribution of reads lenght, like there is in a lot of papers.

    Thanks in advanced

  • #2
    You can do this with Biopieces (www.biopieces.org) using FASTA files as input:

    Code:
    read_fasta -i in.fasta | plot_lendist -k SEQ_LEN -t post -o lendist.ps -x
    You can convert sff files to FASTA format with sff_extract from the MIRA package. I think it is in this bundle: http://sourceforge.net/projects/mira...r.bz2/download


    Cheers,


    Martin

    Comment


    • #3
      Here is a Biopython solution using matplotlib for plotting, taken almost verbatim from the "Histogram of sequence lengths" example in the Biopython Tutorial, but using an SFF file as input:

      Code:
      from Bio import SeqIO
      sizes = [len(rec) for rec in SeqIO.parse("example.sff", "sff-trim")]
      
      import pylab
      pylab.hist(sizes, bins=20)
      pylab.title("%i Roche 454 reads\nLengths %i to %i" \
                  % (len(sizes),min(sizes),max(sizes)))
      pylab.xlabel("Read length (bp, trimmed)")
      pylab.ylabel("Count")
      pylab.show()

      Comment


      • #4
        Thanks a lot for your answers!! For using biopieces and make the plot Do I have to install Ruby and Phyton necessarily?

        Comment


        • #5
          Biopieces have a number of prerequisites including Ruby (and for a few Biopieces, Python as well).



          However, even if the installation of Biopieces is a bit tricky, it is worth while, IMHO!


          Martin

          Comment


          • #6
            Originally posted by maasha View Post
            You can convert sff files to FASTA format with sff_extract from the MIRA package. I think it is in this bundle: http://sourceforge.net/projects/mira...r.bz2/download
            Or from the sff_extract home page, http://bioinf.comav.upv.es/sff_extract/index.html - note this needs Python.

            Comment

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