Question: ploting paired-end reads using GenomeGraphs
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gravatar for Ramzi TEMANNI
10.0 years ago by
Ramzi TEMANNI160
Ramzi TEMANNI160 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]]
idiogram genomegraphs • 538 views
ADD COMMENTlink modified 10.0 years ago by Kasper Daniel Hansen6.4k • written 10.0 years ago by Ramzi TEMANNI160
Answer: ploting paired-end reads using GenomeGraphs
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gravatar for Kasper Daniel Hansen
10.0 years ago by
United States
Kasper Daniel Hansen6.4k 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 > Bioc-sig-sequencing at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
ADD COMMENTlink written 10.0 years ago by Kasper Daniel Hansen6.4k
Hi Kasper, Thanks for your reply, I've take a look at the Reference Manual<http: www.bioconductor.org="" packages="" 2.5="" bioc="" manuals="" genomegra="" phs="" 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 < khansen@stat.berkeley.edu> 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 > > Bioc-sig-sequencing@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > [[alternative HTML version deleted]]
ADD REPLYlink written 10.0 years ago by Ramzi TEMANNI160
library(GenomeGraphs) test <- new("MappedRead", start = 1:10, end = 4:13, strand = rep(c("+", "-"), each = 5)) gdPlot(test, minBase = 1, maxBase = 13) There is no analogue to makeBaseTrack for example. You'll notice that the reads are colored according to strand. All that needs to be done is essentially to have start1, start2, end1, end2 and then draw small rectangle, line, small rectangle, for each read. Kasper On Dec 17, 2009, at 9:14 AM, Ramzi TEMANNI wrote: > Hi Kasper, > Thanks for your reply, > I've take a look at the Reference Manual 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 <khansen at="" stat.berkeley.edu=""> 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 > > Bioc-sig-sequencing at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >
ADD REPLYlink written 10.0 years ago by Kasper Daniel Hansen6.4k
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