On Sun, Aug 16, 2009 at 4:20 AM, Abhishek Pratap <[email protected]>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<[email protected]> 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 > >> > >> _______________________________________________ > >> Bioc-sig-sequencing mailing list > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > > > > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
