Hi Michael
Thanks for a quick revert. Please find my reply under your questions. _Abhi From: [email protected] [mailto:[email protected]] On Behalf Of Michael Lawrence Sent: Wednesday, December 02, 2009 5:51 PM To: Pratap, Abhishek Cc: [email protected] Subject: Re: [Bioc-sig-seq] Plotting Coverage for inhouse genome On Wed, Dec 2, 2009 at 2:31 PM, Pratap, Abhishek <[email protected]> wrote: Hi All After taking an exciting BioC course at FredHutch recently, I am trying to dive into BioC world to make more sense of NGS data. I would also like to thank the entire BioC team present there. You guys were simply great. I appreciate you all patiently answering tons of questions and taught some of the cool things we can do with BioC packages. For my current problem I would like to generate coverage plots for a small bacterial genome. I have the reads imported as a AlignedRead object and I am not sure how to proceed next. The help for the "coverage" method didn't get me very far. I am looking for some pointers to help me resolve the following questions. 1. How to create a RLE list from the AlignRead object using coverage method ? 2. Do I need to pack my reference genome as BSgenome data package in order to do this ? If yes I just have the sequence and no group II mask file. 3. Finally how to plot a RLE list. This is a pretty difficult question to answer. Do you want to see all chromosomes at once (like a karyotype plot)? An overview of entire chromosomes? Or do you want to explore the data in an interactive genome browser? >> For now I am looking for an quick overview of entire genome. This is a small bacterial genome with just one scaffold /super-contig whatever we may call it. For later an interactive session in a genome brower shall be highly useful. There are many packages in Bioconductor for plotting this sort of data, including GenomeGraphs and HilbertVis. For genome browsers, there's rtracklayer and others. For example, with rtracklayer: session <- browserSession() session$coverage <- as(coverage, "RangedData") I will pick one of these method once I am able to form a RangedData object. Thanks! Thanks! -Abhi _______________________________________________ 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
