Helllo, I would like to ask the questions related to featureCounts. I already had the annotation file as .gff3 file. I want to count read pairs for annotated genes based on exons using featureCounts and save the resulting count as .bed file. I wrote the command as below: featureCounts -g genes -t exons -a gencode.annotation.chrX.gff3 -o quantification_genes.bed
The problems are: -my output file always show as: temp_core_00C2932.sam. It is sam file, not bed file as I expected. -my output file always does not show any information of counting.
Could anyone suggest me what is exactly wrong in my command?