Hi Rory,

I am trying diffBind on my ATAC-seq data. And I have difficulties on using db.count() function. I got error message as below.

Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,  : 
  Some read files could not be accessed. See warnings for details.
In addition: Warning message:
no not accessible 

I was wondering whether there is a specifically way to organize the bam file which could be read in the dba project. 

Thank you so much.

Hi Yijing-

The warning message contains the name of where DiffBind thinks the bam file should be, which for some reason is "no". Did you create the DBA object using dba() and a samplesheet? If you could send me a copy of the samplesheet, I'll have a look. You could also send me a copy of DBA itself as well, so I can see how the samplesheet got interpreted.

Cheers-

Rory

Hi Yijing-

First, I realize that I missed your original question because you didn't tag it with DiffBind, only edger -- I get notified of any issues with the DiffBind tag.

I had a look at your samplesheet, and I see the problem: you are entering "no" in the bamControl column, so DiffBind is looking for a file named "no" containing the control reads. If you have no control reads, just leave this column blank, or delete it entirely.

Cheers-

Rory

Hi Rory,

Thank you so much for your reply. I will take your suggestions for trouble shooting.

yijing  

Hi Rory,

Thank you so much. I can't believe that I spend so many time and it just work now.