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). Any pointers in this regard will help a lot. Thanks, -Abhi 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
