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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