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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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error not able to find bam file #19

Closed GoogleCodeExporter closed 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_R1.hg19.bam.bai -O R10.genebody

What is the expected output? What do you see instead?
Done
Analyze bam files and calculate coverageError in 
FUN("/srv/gsfs0/projects/cho/riboseq/bam/R10_R1.hg19.bam.bai"[[1L]],  :
  'filename' is not a BAM file
  file: /srv/gsfs0/projects/cho/riboseq/bam/R10_R1.hg19.bam.bai
Calls: headerIndexBam ... indexBam -> sapply -> sapply -> lapply -> FUN -> .Call
Execution halted

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

Original issue reported on code.google.com by biotechd...@gmail.com on 22 May 2014 at 9:03

GoogleCodeExporter commented 9 years ago 
Hi, you should use "-C /srv/gsfs0/projects/cho/riboseq/bam/R10_R1.hg19.bam" 
instead of "-C /srv/gsfs0/projects/cho/riboseq/bam/R10_R1.hg19.bam.bai".

Original comment by shenli.sam on 22 May 2014 at 9:08