Hello, I am learning how to do RNA-seq analysis following this tutorial:
I'm having a problem generating a table of gene counts using the program featureCounts on my annotation file (GTF) and aligned sequences (BAM).
Here's what I'm typing into the unix shell:
I don't get any errors and the program seems to handle everything ok, here is an example output for one of the files:
BUT when I open my counts.txt file, I don't have any hits. All I get back is a table full of zeros for every gene.
Does anyone know why this is happening?
I'm having a problem generating a table of gene counts using the program featureCounts on my annotation file (GTF) and aligned sequences (BAM).
Here's what I'm typing into the unix shell:
Code:
$ featureCounts -a Homo_sapiens.GRCh38.82.gtf -o counts.txt -t exon -g gene_name -T 4 */accepted_hits.bam
Code:
Process BAM file trimmed_uvb3.fastq_tophat/accepted_hits.bam... || Single-end reads are included. || Assign reads to features... || Total reads : 129858 || Successfully assigned reads : 98419 (75.8%) || Running time : 0.00 minutes
Does anyone know why this is happening?
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