Question: diffBind - bam not accessible
0
gravatar for eli7javasky
3.6 years ago by
European Union
eli7javasky0 wrote:

Hi,

I'm trying to analyze chip-seq histone modification data with diffBind. When I try running diffBind, it tells me that my bam files cannot be accessed. It was able to make the plot based on the peaks so it is able to access my peak files. This is the code I've been trying:

mod=dba(sampleSheet=paste0(args[1]))

plot(mod)  #this works

mod=dba.count(mod, minOverlap=2)

plot(mod)

 

My sampleSheet contains the following columns and all of the location paths are correct (it's a .csv file):

 

SampleID, Condition, Replicate, bamReads, ControlID, bamControl, Peaks, ScoreCol
 

Do you know why it cannot access my bam files? The bam.bai files are in the same location as the bams. Any help would be greatly appreciated. Thank you so much,

Elisheva J

diffbind bam chip-seq • 977 views
ADD COMMENTlink written 3.6 years ago by eli7javasky0

Hi,

Do the paths in your sample sheet contain tildes, by any chance?  (e.g. ~/bam/my_file.bam)?  The release version of DiffBind doesn't process them correctly (it's fixed in devel).  If so, try replacing them with absolute paths.  Also, leading or trailing white space in the filenames will cause problems (also fixed in devel).  If it's neither of those, post or email the sample sheet and I'll take a look at it. 

Cheers,

 - Gord

ADD REPLYlink written 3.6 years ago by Gord Brown590
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