Re: [bedtools-discuss] bedtools multicov

[Aaron Quinlan]

Hi Monica,

With version 2.17.0, I cannot replicate this error with correct file names.  I can only replicate this when I intentionally provide a file that I know doesn't exist.  Are you sure you don't have any typos in the filenames?  What version are you using?

Best,

- Aaron

On Jan 4, 2013, at 3:17 PM, Monica Wu <midnigh...@gmail.com> wrote:

Hi everyone,

I have multiple BAM files that I want to get the read numbers from. I tried using the multicov command like so:

bedtools multicov -bams 1.bam 2.bam -bed ce10.bed > intersect.txt

But I get the error "Could not open input BAM files".

However, when I use the multicov command on each file individually, it works fine. 

Anyone know why that's the case?

[Aaron Quinlan]

Hi Francois,

Sorry for the poor docs.  I am in the middle of (slowly) rewriting the documentation as a website on readthedocs.org.  While the site is not yet complete, here is the current page the multicov command.  I hope this helps.

https://bedtools.readthedocs.org/en/latest/content/tools/multicov.html

- Aaron

quinlanlab.org

On Jan 14, 2013, at 9:31 AM, francois...@gmail.com wrote:

I had the same error. I sorted and indexed my file, and it finally worked. I am quite new to the tool, so I hope I did not do anything stupid there !

Is there any manual page explaining the tool, notably the output ?