Hi Kasper, Thanks for your reply, I've take a look at the Reference Manual<http://www.bioconductor.org/packages/2.5/bioc/manuals/GenomeGraphs/man/GenomeGraphs.pdf>but unfortunately there's no example on how MappedReads class works. If you are familiar with it, could you please send me a quick example on how it works ? Thanks in advance, Regards, Ramzi ----------------------------------------------------------------
On Thu, Dec 17, 2009 at 2:37 PM, Kasper Daniel Hansen < [email protected]> wrote: > There is a MappedRead class, but I think right now it only supports > single-end. It would however be more or less trivial to extend to paired > end reads. I have cc'ed the GenomeGraphs people. > > Kasper > > On Dec 17, 2009, at 8:24 AM, Ramzi TEMANNI wrote: > > > Hi, > > I would be interested in plotting the paired reads in a specific area of > the > > genome to have a nice representation of the distribution of paired reads > . > > Suppose we would like to visualize reads in this area: > > chr7:13730853-14031050 > > i found out that the GenomeGraphs package can provide different > > possibilities for plotting such data > > using the following code : > > library(GenomeGraphs) > > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > ideogram <- makeIdeogram(chromosome = 7) > > genomeAxis <- makeGenomeAxis(add53 = TRUE, > > add35 = TRUE) > > gdPlot(list(ideogram, genomeAxis), minBase = 13730853, maxBase = > 14031050) > > I get a template with the idiogram and an axis of the area of intrest. > > > > How can I add the paired reads to that template (drowing rectangles > > [pos.m1--pos.m2])? > > > > CHR.M1 POS.M1 DIR.M1 CHR.M2 POS.M2 DIR.M2 GAP > > 452475 chr7 13733464 - chr7 13736747 + 3283 > > 310647 chr7 13739099 - chr7 13742564 + 3465 > > 642995 chr7 13740159 - chr7 13743227 + 3068 > > 124021 chr7 13743838 - chr7 13747629 + 3791 > > 145136 chr7 13747724 - chr7 13751470 + 3746 > > 95433 chr7 13752663 - chr7 13756523 + 3860 > > 349071 chr7 13754592 - chr7 13758004 + 3412 > > 578333 chr7 13764031 - chr7 13767173 + 3142 > > 729375 chr7 13793339 - chr7 13796280 + 2941 > > 39128 chr7 13862817 - chr7 13866904 + 4087 > > 621938 chr7 13867663 - chr7 13870756 + 3093 > > 841914 chr7 13870339 + chr7 13870692 - 353 > > 204578 chr7 13873601 - chr7 13877234 + 3633 > > 414932 chr7 13877564 - chr7 13880892 + 3328 > > 450397 chr7 13878852 - chr7 13882138 + 3286 > > 594118 chr7 13880502 - chr7 13883627 + 3125 > > 276694 chr7 13884763 - chr7 13888278 + 3515 > > 389308 chr7 13887051 - chr7 13890410 + 3359 > > 42539 chr7 13895684 - chr7 13899746 + 4062 > > 117314 chr7 13896500 - chr7 13900307 + 3807 > > 251549 chr7 13901220 - chr7 13904774 + 3554 > > 608668 chr7 13915635 - chr7 13918743 + 3108 > > 847653 chr7 13920433 + chr7 13920728 - 295 > > 67139 chr7 13933413 - chr7 13937358 + 3945 > > 182569 chr7 13937777 - chr7 13941450 + 3673 > > 294702 chr7 13938511 - chr7 13941999 + 3488 > > 535133 chr7 13942971 - chr7 13946161 + 3190 > > 515881 chr7 13943523 - chr7 13946735 + 3212 > > 698816 chr7 13951296 - chr7 13954289 + 2993 > > 741044 chr7 13953294 - chr7 13956211 + 2917 > > 237927 chr7 13959649 - chr7 13963225 + 3576 > > 124263 chr7 13961471 - chr7 13965262 + 3791 > > 806523 chr7 13971198 - chr7 13973008 + 1810 > > 342437 chr7 13982437 - chr7 13985858 + 3421 > > 374119 chr7 13985689 - chr7 13989068 + 3379 > > > > Thanks in advance for your suggestion. > > > > Kind regards, > > Ramzi > > ---------------------------------------------------------------- > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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
