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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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Error in plotting #20

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.-bash-4.1$ ngs.plot.r -G hg19 -R genebody -C 
/srv/gsfs0/projects/cho/riboseq/bam/R10_Rluc_control_arsenite_R1.hg19.bam -O 
R10.genebody
.

What is the expected output? What do you see instead?
.Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,  :
  missing value where TRUE/FALSE needed
Calls: plotheat -> ColorBreaks -> seq -> seq.default
Execution halted

Original issue reported on code.google.com by biotechd...@gmail.com on 22 May 2014 at 9:10

GoogleCodeExporter commented 9 years ago 
I'm not sure what happened here. Is it possible for you to transfer this bam 
file to me in private? I'll run some diagnosis. Email: shenli.sam@gmail.com for 
details.

Original comment by shenli.sam on 23 May 2014 at 1:37

GoogleCodeExporter commented 9 years ago 
I have the same issue. It seems to be connected to sam/bam files created by the 
star alignment software. If I do the same thing with Bowtie it seems to work.
Do you have a solution for this already? Other software like samtools, ceas, 
igv, etc. work flawlessly with these files.

Original comment by cark...@gmail.com on 25 Jul 2014 at 11:53

GoogleCodeExporter commented 9 years ago 
We added recognition for Star aligner long time ago...Even if it is a strange 
aligner, ngs.plot is able to proceed and generates a warning message. Which 
version are you using? The newest version should be v2.41.x.

Original comment by shenli.sam on 25 Jul 2014 at 4:48

GoogleCodeExporter commented 9 years ago 
I was still using 2.0.8 because I did not see the message about the new Git 
archive. It works with 2.4.1, so thanks for the info!

One thing I noticed is that the STAR alignment heatmaps show a weird clustering 
effect that was not visible using Bowtie... Any idea why that happens? Is that 
why you think that STAR is strange?

Original comment by cark...@gmail.com on 28 Jul 2014 at 11:54

Attachments:

GoogleCodeExporter commented 9 years ago 
For clarification: i used the following command without clustering.

ngs.plot.r -G mm10 -R tss -C pr_star_h3k4me3/igv/h3k4me3_trim.bam -O 
pr_star_h3k4me3/ngsplot/h3k4me3_tss_total -T h3k4me3_tss_total -L 3000 -FL 150

Using the old ngsplot and bowtie this command resulted in a distribution of 
strongest to weakest tss. Now I get this weird blocking effect, that should 
really not be there. Other steps in my pipeline (which remained the same) are 
samtools sorting of the bam file and samtools removal of duplicates.

Original comment by cark...@gmail.com on 28 Jul 2014 at 12:57

GoogleCodeExporter commented 9 years ago 
Hi,

ngs.plot is not biased towards any aligner. So I don't think it penalizes
the visualization of STAR in any way.

However, I have updated the algorithms for clustering and heatmaps in
upgrade. Particularly, clustering is now based on ranks. There are also a
few new arguments that control the appearance of heatmaps. I do not see
your attachment so I am not able to determine the cause of your problem.

You may want to start a new thread on the discussion forum where you can
insert figures easily.

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 31 Jul 2014 at 4:05