[BioC] [Bioc-sig-seq] ploting paired-end reads using GenomeGraphs

[Kasper Daniel Hansen]

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
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