Question: R visualization package : Genome-wide distribution and orientation of translocations
1
gravatar for Bastien Hervé
11 weeks ago by
Bastien Hervé2.7k
Limoges, CBRS, France
Bastien Hervé2.7k wrote:

Hello,

Any ideas how to create a genome-wide visualization like this one, from this publication ?

nihms322291f2

I read the M&M and the Extended Protocol Procedures but they just mention R language...

I contacted the first author but did not get an answer yet...

This is a genome-wide representation of translocation events, with a bin size of 5 million bases, one event in a bin is a black dot, 5 events in a bin is a red dot etc...

I tried to use chromPlot and it works well, I got histograms of events. It's cool but I do have like 500 events on the same bin and casual events randomly that I can barely see due to the 500 events...

I'm interested in the events count aggregation using dots which I can not find yet over the R packages...

Thanks !

R • 181 views
ADD COMMENTlink modified 7 weeks ago by Biostar ♦♦ 20 • written 11 weeks ago by Bastien Hervé2.7k

any raw /plain text data available ?

ADD REPLYlink written 11 weeks ago by Pierre Lindenbaum115k

Authors did not shared fastq files of theirs experiments. Futhermore, to get the translocation visualization like above, they used LAM-HTGTS technique and they did not mention all parameters and filters in the publication. Sadly, I can't share my data here, it is not public yet. But I got a GRanges structure in which each line is a translocation junction (one black point).

ADD REPLYlink written 11 weeks ago by Bastien Hervé2.7k

I'm interested in the events count aggregation using dots which I can not find yet over the R packages...

bedtools https://bedtools.readthedocs.io/en/latest/content/tools/groupby.html ?

ADD REPLYlink written 11 weeks ago by Pierre Lindenbaum115k

Thanks Pierre, but I'm interested in the dots visualization not in the count aggregation step

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Bastien Hervé2.7k

Try to contact the author of the publication for the source code of this plot.

ADD REPLYlink written 7 weeks ago by Nicolas Rosewick7.0k

I contacted the first author but did not get an answer yet...

I have contacted first, second authors and an other one in the middle of the author list but I got no answer... (1 month ago)

ADD REPLYlink written 7 weeks ago by Bastien Hervé2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1670 users visited in the last hour