Hi all

I am trying to learn how to use Rsubread.

I have a bam file from a bacterial sequencing project, and a related gtf file.  I want to count hits to each gene and have been using the following command:

fc_External<-featureCounts("bamFIle.bam", annot.ext= "gtfFile.gtf", isGTFAnnotationFile=TRUE, GTF.featureType="CDS",useMetaFeatures=TRUE,allowMultiOverlap=TRUE,nthreads=3,countMultiMappingReads=TRUE)

The analysis returns 0% successfully assigned reads.

Can you indicate where I might be going wrong?

Many thanks

Ross

I have solved the problem.

There was a small difference in the chromosome notation in the BAM and GTF files.

Thanks for your attention.

Ross

Hi, I am facing same problem. can you please guide me on that problem?

Thanks