RSeQC GeneBody function error. Stops at R Script Step

Question

[achamess]

Hi all,

When I try to run the GeneBody distribution function in RSeQC, it aborts with this error. Can anyone help me make sense of this?

@ 2017-02-16 18:32:36: Read BED file (reference gene model) ...
@ 2017-02-16 18:32:43: Total 36855 transcripts loaded
@ 2017-02-16 18:32:43: Get BAM file(s) ...
Warning: AC-L1Aligned.bam.bai does not exist! Skip it.
Sample  Skewness
@ 2017-02-16 18:32:43: Running R script ... 
null device 
 1

Answer 1

[Lina F]

Usually, the "null device 1" line means that R did open the device for drawing.

Did you check that the pdf file was not created?

Also, if you don't set up your output prefix option correctly, the file might start with a period, which makes it look invisibe to a Linux or Mac OSX terminal.

So if you are on a Mac or a Linux system, also run ls -la in the directory. If you do see a pdf file where the file name starts with a period, change the name and then the file should be visible in the GUI browser as well.

Edit: I just saw that the bai file doesn't exist. Fix that problem first and then check again to see if the PDF gets created.

[achamess]

Thanks! There is a PDF file, but it doesn't open. It's like 3kb, so I'm assuming there is nothing in it. I didn't know the BAM files needed an index, according to the manual. I'll do that and see if it helps.

[achamess]

That was the trick! Thanks. There needs to be bam index files in the same directory.