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jlw-laputa / ngsplot

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Support for single-base DNA methylation seq data #18

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
5mC and 5hmC are common DNA methylations. Single-base methylation seq data are 
quite different from histone modification ChIP-seq data in the way of how the 
methylation information is encoded in a bam file. Supporting for this kind of 
data can make ngs.plot much more useful for DNA methylation researchers.

Original issue reported on code.google.com by shenli.sam on 22 May 2014 at 1:39

GoogleCodeExporter commented 9 years ago 
I agree, but perhaps some temporary solution is available.

If one generated their own alignment matrix ... could one use replot.r to 
create a heatmap???  In the output zip files after using ngsplot.r, one can 
find hm, sem, and avgprof text files.  There are also heatmap and avgprof Rdata 
files.  If one wanted to only make a heatmap, would the avgprof Rdata and sem 
/avgprof text files be required to be stored in the zip file?  Probably not.  
The hm text file is likely required, but what about the heatmap Rdata file?  
Not sure.  

The hm file has 4 columns: gid, gname, tid and strand.  Are these columns 
always present?  I assume the gname is required to be unique.  I also know gid 
and tid can be NA. The rest of the columns are labeled 1 .. the total #of bins, 
which is 100.  Can this be changed?

Thanks for your time and consideration.

Original comment by ckcollin...@gmail.com on 25 Sep 2014 at 5:53

GoogleCodeExporter commented 9 years ago 
You need to modify the RData files. The text files are not used by
ngs.plot. - Li

-- 
Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
#################
ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/
Want ChIP-seq differential analysis? Use:
https://code.google.com/p/diffreps/

Original comment by shenli.sam on 25 Sep 2014 at 8:00

GoogleCodeExporter commented 9 years ago 
Thanks for your quick response.

Could you dig out the relevant source code for making the heatmap Rdata file? 

I am better at Perl than R.  I use R somewhat frequently but lack experience in 
setting up many data structures. 

-Clay

Original comment by ckcollin...@gmail.com on 25 Sep 2014 at 11:08