rsubread featurecounts returns 0% successfully assigned reads
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ross.chapman ▴ 10
@rosschapman-7326
Last seen 9.2 years ago
Australia

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

rsubread • 3.5k views
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ross.chapman ▴ 10
@rosschapman-7326
Last seen 9.2 years ago
Australia

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

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amoltej ▴ 10
@amoltej-7192
Last seen 6.5 years ago
Australia

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

Thanks

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

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