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?
You can use the 'chrAliases' option in featureCounts to match chromosome names in your BAM files with those in your annotation.