frequency distribution plot

[alessandra85]

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

[maasha]

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

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

[maubp]

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:

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()

[alessandra85]

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

[maasha]

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

http://code.google.com/p/biopieces/wiki/Installation#Prerequisites

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


Martin

[maubp]

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.