On Sun, Aug 16, 2009 at 4:20 AM, Abhishek Pratap <abhishek.vit@gmail.com>wrote:

> Hi Michael
>
> Thanks for your reply. Well basically we have downloaded the human
> reference RNA set from NCBI and using the same to asses coverage. It
> is a rough estimate to help our collaborators decide on hwo much
> sequencing they need to do in order to reach required coverage for SNP
> calling. So till now I have calculated coverage using the ELAND
> alignment results. I am now looking for ways to plot it so that
> biologists could interpret it easily.
>
> So I have many hashes(perl), each having a "numerical" coverage data
> obtained from Next generation sequencing data analysis. Now each
> hash/list may have couple of hundred to thousands entry "contig_name
> => coverage".  What I want to do is to plot a histogram for each
> hash/dataset.  "Coverage v/s Count of contigs with coverage > #N " ( N
> has to be binned according to the data size).
>

Abhi,

It sounds like you already have the data that you want to plot, but in
perl?  If so, you can simply write out the numeric data to a file and then
read it into R.  R has the hist() function which will do the binning, etc.,
and the read.table() function to read in the data.

If I am missing something, you will probably need to clarify what details
you need to still do to accomplish your task.

Sean


> On Thu, Aug 13, 2009 at 4:30 AM, Michael
> Dondrup<Michael.Dondrup@bccs.uib.no> wrote:
> > Hi Abhi,
> >
> > just a short comment. To assess coverage the crucial point is to know the
> > length of your target sequence, thus the length of the
> > human transcriptome. Then e.g. the Lander-Waterman statistic can be
> > computed. So how could the length of total mRNA
> > be calculated. I think this is not possible, is it?
> >
> > Best
> > Michael
> >
> > Am 12.08.2009 um 23:59 schrieb Abhishek Pratap:
> >
> >> Hi All
> >>
> >> Just wondering if a package/R function exists which can help us answer
> >> the following question.
> >>
> >> We are trying to assess the right amount of sequencing we need to do
> >> in order to cover the human transcriptome.  For the runs we have
> >> already done, we have the reads aligned to human mrna ref using ELAND.
> >> We would like to plot graphs per lane to show the percent coverage of
> >> human transcriptome.
> >>
> >> Let me know if it is not clear, I can reframe or explain in detail.
> >>
> >> Thanks,
> >> -Abhi
> >>
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> >
> >
>
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