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I keep getting flat metaplots from the ngsplot? Genome loading issue or data issue? #39

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?

1. downloaded and installed the arabidopsis genome files 

ngsplotdb.py install ngsplot_Tair10_....gz

genome installed

2. run ngs.plot.r

ngs.plot.r -G Tair10 -R genebody -C /path/to/sorted_indexed/bamfile.bam -O 
output 

3.

What is the expected output? What do you see instead?

The expected output is any kind of non-flat metaplot! I get a flat unchanging 
metaplot across any region I choose genebody, tss tes etc.... but I don't get 
any errors that I can tell.

What version of the product are you using? On what operating system?

I've tried the most recent ngsplot and several of the older ones back to 2.00. 
I'm using a linux ubuntu 14.04 OS 

Please provide any additional information below.

it seems when I run the program I get large counts from the count files but 
both the plot files: heatmap and profile for genebody, tss, tes and anything 
else I try are completely flat as though no data has mapped there! I feel like 
its probably a genome issue but I don't know what I've done wrong in loading 
it! Any advice on what to check out?

Best Regards
DS

Original issue reported on code.google.com by sandman2...@gmail.com on 18 Feb 2015 at 3:50

GoogleCodeExporter commented 9 years ago 
I've now gotten further see below 

Dear Shen Lab,
I wanted to first thank you all for all your hard work on such a useful tool! 
Unfortunately in my hands I cannot get it give me anything but flat plots.

I believe all genomes and files and dependencies are correct and I run:

ngs.plot.r -G Tair10 -R genebody -C my_sorted_indexed.bam -O output

It reports a flat plot an empty heatmap, no errors....
I found this post by Dr. Toshiyuki Sone where he was able to get his plots 
working by altering the bam files:

https://groups.google.com/forum/#!searchin/ngsplot-discuss/flat$20plot/ngsplot-d
iscuss/mWxJIYRlz_w/tcnQY2mGXkcJ

I believe this may be the same issue for me in that the: .Rdata files have 
lowercase  chr1, chr2 ....

and my bam files have Chr1 Chr2 .... I've tried many methods but cannot get 
ngs.plot.r to take my altered bam files

it mostly reports: Error: Read XZ5_AAG_edited.bam error: Inconsistent 
chromosome names in bam file. Check bam header.

Although I am fairly sure that the bam files are consistent. is there some way 
to alter either bam files or the .Rdata files that will allow me to profile my 
reads?

Best
DS

Original comment by sandman2...@gmail.com on 20 Feb 2015 at 7:49

GoogleCodeExporter commented 9 years ago 
Figured it out! Thanks for such an amazing program. I had to remake my index 
files to contain small chr1,chr2 instead of large Chr1, Chr2 ... because the 
small chr1 .. are the ones that are read by your Rdata files. So far the 
results look very promising for our work. Thanks for all your help.

Best
DS

Original comment by sandman2...@gmail.com on 23 Feb 2015 at 11:10