When I used dba.cout with DiffBind， the following error occurred.

Code should be placed in three backticks as shown below

library(DiffBind)
library(parallel)
dbObj <- dba(sampleSheet="SampleSheet.csv")
dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE)

The following error occurred

Error in if (sum(tokeep) < length(tokeep)) { : 
missing value where TRUE/FALSE needed

The bam files were obtained after bowtie2 alignment, and the bed files were obtained using AutoCirc. The last line of these bed files was not truancated.

Here are some related figures.

Here is the head of bed file

Hey,

Did you make the index of the BAM files?

If not, this can sometimes produce the error code you received.

Continuing from the duplicated question at BioStars (https://www.biostars.org/p/9505794/#9506872):

Is there a reason that the .bam files have "unmapped" in their filenames? If you are trying to count unmapped reads I would expect that to fail!

For me to see exactly what is happening I'd need access to some or all of your data, including

• the DBA object dbObj prior to the call to dba.count(), saved using dba.save()
• the four .bam and .bai files

If you can do that, email me a link where I can download it.