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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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One line gene list => crash #4

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi !

I am looking for a solution to get a coverage plot for individual genes, where 
y shows the absolute coverage count (not in % of million) and x would be the 
exons of a gene.

I tried ngsplot, but it seems to cumulate genes from the genelist into a single 
plot, and dies if i only give it one gene in the list:

worker@server:~/analysis/2013-05-13_AML/bam$ cat genes.txt 
CEBPA
worker@server:~/analysis/2013-05-13_AML/bam$ cat run.txt 
IonXpress_022_rawlib_PTRIM.bam  genes.txt   "Test"
worker@server:~/analysis/2013-05-13_AML/bam$ ngs.plot.r -G hg19 -R genebody -C 
run.txt -O testa
Loading R libraries.....Done
Configuring variables...
Using database:
/home/worker/software/ngsplot/ngsplot/database/hg19/hg19.ensembl.genebody.protei
n_coding.RData
Done
Analyze bam files and calculate coverage.Done
Plotting figures...Error in if (nrow(enrichCombined) > 1) { : argument is of 
length zero
Calls: plotheat
Execution halted
worker@server:~/analysis/2013-05-13_AML/bam$

It works fine if i add another line to the genes.txt file

am i doing something wrong ?

Original issue reported on code.google.com by karl.kas...@gmail.com on 25 Jun 2013 at 3:24

GoogleCodeExporter commented 9 years ago 
This problem should have been fixed in the newest versions. I'll close this 
issue.

Original comment by shenli.sam on 19 Dec 2013 at 4:24

GoogleCodeExporter commented 9 years ago

Original comment by shenli.sam on 19 Dec 2013 at 7:05

GoogleCodeExporter commented 9 years ago 
I have exactly same error. So that means it has not been fixed in newer version 
or it simply recurred.
thanks

Original comment by kanwar...@gmail.com on 7 May 2014 at 2:17

GoogleCodeExporter commented 9 years ago 
Same here I tried it and it is giving me same error??

Original comment by gupta567...@gmail.com on 12 May 2014 at 5:53

GoogleCodeExporter commented 9 years ago 
This problem has been fixed in the current develop branch.

Original comment by shenli.sam on 20 May 2014 at 9:24